Cited Structures: list of articles citing SSGCID structures

The SSGCID has begun tracking the number of publications by the scientific community which reference Center structures. This list has been manually reviewed and contains only articles that refer to SSGCID structures, whether in the main text, figure captions or supplementary material. Publications by SSGCID authors are excluded from this list.


This list was obtained from Google Scholar searches using an API provided by Christian Kreibich.



# PDB Additional SSGCID structures cited Link Title Year Citation Highlighted Abstract
1 6wps 7jvc, 7jva, 7jv6, 7jx3, 7k45, 7jw0 Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies 2021 J Chen, K Gao, R Wang, GW Wei- Chemical science, 2021 - pubs.rsc.org Our predictions are built from the X-ray crystal structure of SARS-CoV-2 S protein and ACE2 ( PDB 6M0J), 57 and various antibodies (PDBs 6WPS , 66 6XC2, 58 6XC3, 58 6XC4, 58 6XC7, 58 6XE1, 64 6XEY, 83 6XKP, 72 6XKQ, 72.
2 4q6u - PAS domains in bacterial signal transduction 2021 EC Stuffle, MS Johnson, KJ Watts- Current Opinion in Microbiology, 2021 - Elsevier ad) PAS monomer structures : (a) The PAS structural prototype photoactive dimer bound to heme cofactor (Fe 3+ , PDB : 4HI4, [25]) and a liganded monomer with cyanomet heme (Fe 3+ -CN, PDB : 3VOL, [31 For clarity, b-type heme is only shown bound to the liganded structure
3 3qhx 3qi6 Pharmacophore-Guided Identification of Natural Products as Potential Inhibitors of Mycobacterium ulcerans Cystathionine -Synthase MetB 2021 SK Kwofie, NNO Dolling, E Donkoh, GM Laryea, L Mosi- Computation, 2021 - mdpi.com For the study, chain A of each 3D crystal structural coordinate file was used. Two experimentally elucidated structures of CGS MetB from M. ulcerans are available. The structure with PDB ID 3QI6 is bound covalently to PLP (cofactor) and the other with PDB ID 3QHX is bound
4 6xdh - 3D-Scaffold: Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds. 2021 RP Joshi, N Gebauer, N Kumar, M Bontha- bioRxiv, 2021 - biorxiv.org generates 3D coordinates of the molecules with a given core structure ; (II) It works equally 3 reasonable molecules even with small training datasets due to the robust architecture of the (Mpro) and a SARS-CoV-2 non- structural protein endoribonuclease (NSP15). ... As a test case example, we generated non-covalent inhibitors for the SAR-CoV-2 non-structural protein endoribonuclease (NSP15) target (PDB ID: 6XDH) by optimizing Exebryl-1 based compounds
5 3qh4 - Protein Engineering for Enhanced Enantioselectivity of Carboxylesterase Est924 Toward Ethyl 2-Arylpropionates 2021 X Liu, M Zhao, X Fan, Y Fu - 2021 - researchsquare.com Enhancement of the enantioselectivity of carboxylesterase A by structure -based mutagenesis. J Biotechnol Page 13. Page 13/14 PDB entry A1 A2 B1 B2 Est924 I203 A203 G208 I212 3H17 M193 V194 G198 M202 3QH4 A209 F210 A214 M218 3WJ1 F197 L198 H202 F206
6 6nb3 - Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM 2021 C Xu, Y Wang, C Liu, C Zhang, W Han- Science, 2021 - advances.sciencemag.org For the FP region, we first built the homology model by the Modeller tool within Chimera by using the MERS-CoV S structure (PDB: 6NB3) as template (2, 58, 59) and then used Rosetta to refine this region against the density map
7 6vyb - Metal-Bound Methisazone; Novel Drugs Targeting Prophylaxis and Treatment of SARS-CoV-2, a Molecular Docking Study 2021 A Abdelaal Ahmed Mahmoud M Alkhatip- International Journal of, 2021 - mdpi.com SARS-CoV-2 currently lacks effective first-line drug treatment. We present promising data from in silico docking studies of new Methisazone compounds (modified with calcium, Ca; iron, Fe; magnesium, Mg; manganese, Mn; or zinc, Zn) designed to bind more strongly to key proteins ... We found that the highest binding interactions were found with the spike protein (6VYB), with the highest overall binding being observed with Mn-bound Methisazone at −8.3 kcal/mol,
8 4hr2 - Structures of radial spokes and associated complexes important for ciliary motility 2021 M Gui, M Ma, E Sze-Tu, X Wang, F Koh- Nature Structural &, 2021 - nature.com In motile cilia, a mechanoregulatory network is responsible for converting the action of thousands of dynein motors bound to doublet microtubules into a single propulsive waveform. Here, we use two complementary cryo-EM strategies to determine structures of the major
9 5eks - In-silico three dimensional structure prediction of important Neisseria meningitidis proteins. 2021 M Ali, M Aurongzeb, Y Rashid- Pakistan Journal of, 2021 - search.ebscohost.com Chain A of 3-dehydroquinate Synthase from Acinetobacter Baumannii in complex with NAD+ with PDB id 5EKS (to be published) was selected as a template structure . The template had 98% query coverage and 56% sequence identity with the target sequence
10 6ws6 - Insights into Innate Immune Response Against SARS-CoV-2 Infection 2021 A Huanu, AM Georgescu, AV Andrejkovits- Revista Romn de, 2021 - sciendo.com The NET structure made by activated neutrophils and mediated by reactive oxygen species bacterial lipopolysaccharides (LPS), flagella, cilia, bacterial unmethylated DNA, or viral structures like dsARN or In addition, sev- eral structural and non- structural SARS-CoV-2 proteins
11 5dvw - Docking-Based Screening of Cell-Penetrating Peptides with Antiviral Features and Ebola Virus Proteins as a Drug Discovery Approach to Develop a 2021 E Raoufi, B Bahramimeimandi- Viral, 2021 - intechopen.com The potential reservoirs of EBOV RNA are three species of African fruit bats [3]. The genome of this virus contains a negative-strand RNA that encodes six structural and one non- structural proteins, which can be employed as potential drug targets, including transmembrane ... The structures of GP (PDBID: 5JQB), VP35 (PDBID: 3FKE), VP24 (PDBID: 4M0Q), VP30 (PDBID: 5DVW), VP40 (PDBID: 4LDB) and NP (PDBID: 4Z9P) proteins of EBOV were collected from Protein Data Bank
12 6ws6 - A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice 2021 DR Martinez, A Schaefer, S Gobeil, D Li, G De la Cruz- bioRxiv, 2021 - ncbi.nlm.nih.gov Open in a separate window. Figure 3. Cryo-EM structure of DH1047 The other antibodies and shown as transparent surfaces: C105 (pale cyan, Class 1, PDB ID: 6XCN and 6XCA), DH1041 (light blue, Class 2, PDB ID: 7LAA), S309 (wheat, Class 3, PDB ID: 6WS6 and 6WPT
13 6nb3 6q04 Molecular mechanisms behind anti SARS-CoV-2 action of lactoferrin 2021 M Miotto, L Di Rienzo, L B- Frontiers in, 2021 - internal-journal.frontiersin.org Structural studies determined the structures of such protein both in free form and bound to ACE2 of the ACE2 receptor with SARS-CoV-2 spike receptor-binding domain, RBD ( PDB id: 6m17 ... The 10 structural analogs (as identified by TM-align Zhang and Skolnick (2005)) found by I-tasser are PDB id: 5X58, 6NZK, 6NB3, 3JCL, 5I08, 6CV0, 5SZS, 5WRG , 6UTK, 6B7N. The first (out of five) model returned
14 6pqh - Structural study of the N-terminal domain of human MCM8/9 complex 2021 J Li, D Yu, L Liu, H Liang, Q Ouyang, Y Liu- Structure, 2021 - Elsevier Journal home page for Structure . Article. Structural study of the N-terminal domain of human MCM8/9 complex Show more Share. Cite Highlights. The heterohexameric NTD structure combined crystal structures with cryo-EM map. ...Some other structures with less than 2.0 Å RMSD include DNA-directed DNA polymerase III (PDB: 3F2B), asparagine-tRNA ligase (PDB: 6PQH), replication protein A (PDB: 2K5V), telomerase-associated protein
15 3u0d - Acute phase 1-acid glycoprotein as a siderophore-capturing component of the human plasma: A molecular modeling study 2021 SA Samsonov, F Zsila, M Maszota-Zieleniak- Journal of Molecular, 2021 - Elsevier JavaScript is disabled on your browser. Please enable JavaScript to use all the features on this page. Skip to main content Skip to article
16 5vpq - Conserved residues Glu37 and Trp229 play an essential role in protein folding of lactamase 2021 A Chikunova, MP Manley, M Ud Din Ahmad- The FEBS, 2021 - Wiley Online Library (2013). Cation- Interactions in -Lactamases: The Role in Structural Stability, Cell Biochem. Biophys. 66, 147155 [49] RP Joosten, F. Long, GN Murshudov & A. Perrakis. (2014). The PDB -REDO server for macromolecular structure model optimization, IUCrJ. 1, 213220 ... Pro226-Trp229-Pro251-Pro252-(Phe287) chain: β-lactamase from Burkholderia phymatum—gold (5VPQ), ...
17 2lwk - Light-Driven Cascade Mitochondria-to-Nucleus Photosensitization in Cancer Cell Ablation 2021 KN Wang, LY Liu, G Qi, XJ Chao, W Ma, Z Yu- Advanced, 2021 - Wiley Online Library Herein, a light-driven, mitochondria-to-nucleus cascade dual organelle cancer cell ablation strategy is reported. structure of BT-Ir and DNA structure (5-CAATCGGATCGAATTCGATCCGATTG- 3, PDB code: 5ju4) and RNA structure (5- GAGUAGAAACAAGGCUUCGG CCUGCUUUUGCU-3, PDB code: 2lwk ) using AutoDock 4.2
18 6q05 - Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network 2021 S Majumder, D Chaudhuri, J Datta, K Giri- Journal of Molecular Graphics, 2021 - Elsevier 2.1. Protein structure retrieval. All the X-ray crystal structures for SARS-CoV-2, SARS-CoV and MERS-CoV S proteins in the lying state were taken from protein data bank [21]. The corresponding PDB IDs are 6VXX, 5X58 and 6Q05 respectively [11,22,23]
19 6xdh - SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets 2021 AF Alsulami, SE Thomas, AR Jamasb- Briefings in, 2021 - academic.oup.com release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures , our group ... (v) Nsp15 (Uridylate specific endoribonuclease)—PDB Id: 6XDH.
20 3nwo - The rise and fall of anandamide: processes that control synthesis, degradation, and storage 2021 RG Biringer- Molecular and Cellular Biochemistry, 2021 - Springer This manuscript discusses the key enzymes in AEA homeostasis, in terms of structure , reaction specificity, enzymatic activity, regulation, and tissue and cellular expression patterns with a focus on the human isoforms involved. ... No X-ray structures or posttranslational modifications have been reported. There are two potential structural model templates suggested on the SWISS-MODEL website [14], template 3nwo.1.A and template 5mxp.1.B. hABHD4 is produced
21 6wps - SARS-CoV-2 receptor binding mutations and antibody mediated immunity. 2021 M Mejdani, K Haddadi, C Pham, R Mahadevan- BioRxiv, 2021 - biorxiv.org 39 ( PDB : 7JMP), CV07- 250 ( PDB : 6XKQ), P2B-2F6 ( PDB : 7BWJ), CV07-270 ( PDB : 6XKP), BD-368-2 ( PDB : 7CHE), and S309 ( PDB : 6WPS ) 53 Laskowski, RA PDBsum: summaries and analyses of PDB structures Fig.1: Structure of SARS-CoV-2 RBD bound to ACE2 receptor
22 4nps - Structural basis for selective AMPylation of Rac-subfamily GTPases by Bartonella effector protein 1 (Bep1) 2021 N Dietz, M Huber, I Sorg, A Goepfert- Proceedings of the, 2021 - National Acad Sciences Skip to main content. Main menu. Home; Articles: Current; Special Feature Articles - Most Recent; Special Features; Colloquia; Collected Articles; PNAS Classics; List of Issues. Front Matter: Front Matter Portal; Journal Club. News: For
23 6cy1 - Essential biochemical, biophysical and computational inputs on efficient functioning of Mycobacterium tuberculosis H37Rv FtsY 2021 MK Ekka, LS Meena- International Journal of Biological Macromolecules, 2021 - Elsevier FtsY is comprised of helices, but this structural pattern was shown to change these ligands cause significant conformational change by variating the secondary structure to transduce GTP-binding proteins. SRP signal recognition particle. PDB protein data bank. fts filamentous
24 4k9d - Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora 2021 AM Perez, JA Wolfe, JT Schermerhorn, Y Qian- RSC Advances, 2021 - pubs.rsc.org The PDB validation server shows this structure to be typical of structures of comparable resolution in measures of R and number of Ramachandran, sidechain and real-space R-value Z score (RSRZ) outliers ( PDB ID 6PX2) The model used for molecular replacement was 4K9D
25 5ig2 3tjr Structural Genomics of Infectious Agents 2021 JS Alenazi - 2021 - search.proquest.com 4 1.3.5 Deposition of Structure in PDB ..... 4 identity to SDR from B.phymatum ( 5ig2 ) .... 45 S.3.2 Targeted approach of structure genomics can be applied to select the biologically important proteins
26 4xgi - Rational engineering of Acinetobacter tandoii glutamate dehydrogenase for asymmetric synthesis of l-homoalanine through biocatalytic cascades 2021 L Wang, S Diao, Y Sun, S Jiang, Y Liu- Catalysis Science &, 2021 - pubs.rsc.org on the crystal structure of GluDH from Burkholderia thailandensis ( PDB ID: 4XGI , resolution: 2.0 ) in symbiosum ( PDB ID: 1AUP and 1BGV) and GluDH from Corynebacterium glutamicum ( PDB ID: 5IJZ amino acid may cause loss of the inherent stability of the hydration structure
27 3swt - Virus-associated organosulfur metabolism in human and environmental systems 2021 K Kieft, AM Breister, P Huss, AM Linz, E Zanetakos- bioRxiv, 2021 - biorxiv.org oxygen binding (eg WH and H) (Knauer 198 et al., 2012). Conserved amino acid residues that are not functional are likely preserved for 199 structural features. The retention of AMGs on viral genomes despite strong selective ... Annotations of functional amino acid residues were labeled according to the Protein Data Bank (PDB, accessed January 2019) (Berman et al., 2000) with the following identification numbers: 4BZQ and 4BZP (CysC), 2GOY (CysH), 3ZEI (CysK), 3SWT (TauD), and 1RG9 (MetK).
28 6nb8 - Epitope profiling of coronavirus-binding antibodies using computational structural modelling 2021 SA Robinson, MIJ Raybould, C Schneider, WK Wong- bioRxiv, 2021 - biorxiv.org Analysis of SARS-CoV-2antibody structural complexes A total of 48 antibodies and 12 nanobodies had at least one published solved X-ray crystal structure in complex to the spike receptor binding domain (RBD, see Table S1 and Table S2 for names and PDB codes), while
29 6q04 - A comparative study of human betacoronavirus spike proteins: structure, function and therapeutics 2021 J Verma, N Subbarao- Archives of virology, 2021 - Springer Coronaviruses are the paradigm of emerging 21st century zoonotic viruses, triggering numerous outbreaks and a severe global health crisis. The current COVI.
30 6aqz - Crystal structure of a GDP6OMe4ketoLxyloheptose reductase from Campylobacter jejuni 2021 JH Kim, A Hofmann, JS Kim- Proteins: Structure, Function, and, 2021 - Wiley Online Library Page 9. Discussion Comparison with other related proteins The crystal structure of Camylobacter MlghC revealed a two-domain architecture commonly found in 36.7; rmsd 1.9 ) and Naegleria fowleri ( PDB ID 6AQZ ; Z-score 34.3; rmsd 2.3 ), and GDP-4-keto-6
31 6mg6 - Nitrilase: a promising biocatalyst in industrial applications for green chemistry 2021 JD Shen, X Cai, ZQ Liu, YG Zheng- Critical Reviews in, 2021 - Taylor & Francis 6I00), Saccharomyces cerevisiae ( PDB : 4H5U and 1F89), Pyrococcus abyssi ( PDB : 3KLC), Helicobacter pylori ( PDB : 6MG6 ) and Synechocystis ( PDB : 3WUY) has been obtained However, with most of the nitrilases, the crystal structure had been resolved, came from eukaryotes
32 5i1f - Bacillus subtilis YngB contributes to wall teichoic acid glucosylation and glycolipid formation during anaerobic growth 2021 CH Wu, J Rismondo, RML Morgan, Y Shen- Journal of Biological, 2021 - ASBMB Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom The crystal structure of YngB revealed that the protein has the typical fold and all necessary active site features of a functional UGPase
33 3uam - Effectors With Chitinase Activity (EWCAs), a family of conserved, secreted fungal chitinases that suppress chitin-triggered immunity 2021 J Martnez-Cruz, D Romero, J Hierrezuelo- The Plant, 2021 - academic.oup.com Phytopathogenic fungi secrete effectors with chitinase activity to break down immunogenic chitin oligomers and suppress plant immunity. The other models are 3D models of crystallized proteins from Hypocrea jecorina (2VTC, glycoside hydrolase family 61 member), A. oryzae (4MAH, lytic poly- saccharide monooxygenase), E. faecalis (4A02, chitinase), and Burkholderia pseudomallei (3UAM, chitin-binding domain)
34 6u94 - Genome sequencing of 196 Treponema pallidum strains from six continents reveals additional variability in vaccine candidate genes and dominance of Nichols clade 2021 NAP Lieberman, MJ Lin, H Xie, L Shretha, T Nguyen- bioRxiv, 2021 - biorxiv.org guided by the top 1-7 templates for each target. We used the following templates in modelling each target: TP0136 used 4a2l and 5oj5; TP0326 used 4k3b and 5d0o; TP0548 used 6h3i; TP0966 used 1yc9, 3d5k, 4k7r, 4mt0, 4mt4, 5azs, and 6u94; TP0967 used 1yc9, 3d5k, 5azp, 5azs, and 6u94.
35 6nbo - Synthesis and investigation of heterocyclic systems as pharmacological agents with conformational study and surface activity 2021 R El-Sayed, I Althagafi, M Morad, SM El-Bahy- of Molecular Structure, 2021 - Elsevier The structure of recent products was illustrated by IR and 1 HNMR spectra a) and virtual simulation was accomplished upon harmful pathogen-protein as co-crystalline PDB file 3coi, 5ahi, 6nbo and 6ocr co-crystal proteins obtained from Protein Database (RCSB PDB : Homepage
36 6q04 - Evolutionary selectivity of amino acid is inspired from the enhanced structural stability and flexibility of the folded protein 2021 SJA Rao, NP Shetty- Life Sciences, 2021 - Elsevier Evolutionary selectivity of amino acid is inspired from the enhanced structural stability and flexibility of the folded protein certain positions is governed by a well-orchestrated feedback mechanism, which follows increased stability and flexibility in the folded structure compared to
37 5vp5 - Developing a macromolecular crystallography driven CURE 2021 KJ McLaughlin - 2021 - aca.scitation.org While these protein x-ray crystallography structures are key to allowing students to CURE that could expose and excite a next generation of potential structural scientists 3 3. KJ McLaughlin, Understanding structure : A computer-based macromolecular biochemistry lab activity, J
38 6wpt - Hyaluronic Acid-2-Deoxy-D-Glucose Conjugate Act as a Promising Targeted Drug Delivery Option for the Treatment of COVID-19 2021 R Thirumalaisamy, V Aroulmoji- International, 2021 - hal.archives-ouvertes.fr of 2DG and HA-2DG was submitted to Online SMILES convertor and Structure file generator proteases Mpro (6LU7), papain like protease PLpro (6W9C), spike protein ( 6WPT ), RNA dependent RNA polymerase (6M71) was retrieved from RCSB PDB database (https
39 3ijp - Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus 2021 S Pote, S Kachhap, NJ Mank, L Daneshian- et Biophysica Acta (BBA, 2021 - Elsevier This paper focuses on structural and mechanistic studies of DapB The structure for DapB has been determined from various bacterial species including Escherichia coli [14], Bartonella henselae [15 Fig. 2. (A) Tetrameric assembly of DapB from V. vulnificus ( PDB ID: 5TEN)
40 6vyb - Combination and tricombination therapy to destabilize the structural integrity of COVID-19 by some bioactive compounds with antiviral drugs: insights from 2021 HR Abd El-Mageed, DA Abdelrheem, SA Ahmed- Structural Chemistry, 2021 - Springer SARS-CoV-2 main protease ( PDB ID: 6LU7), (5b) SARS-CoV-2 spike protein domain ( PDB ID: 6VYB ), and (5c) human entry receptor ACE2 ( PDB ID: 1R42 validation was carried out using our previously published work [36] with re-docking of the co-crystal structure (N3) as an
41 5i0p - Metallo--lactamase domain-containing protein 2 is S-palmitoylated and exhibits acyl-CoA hydrolase activity 2021 MIP Malgapo, JM Safadi, ME Linder- Journal of Biological Chemistry, 2021 - Elsevier JavaScript is disabled on your browser. Please enable JavaScript to use all the features on this page. Skip to main content Skip to article
42 6wpt - The SARS-CoV-2 spike variant D614G favors an open conformational state 2021 RA Mansbach, S Chakraborty, K Nguyen- Science, 2021 - advances.sciencemag.org 1 Structural representation of the Spike protein. (A) The Spike complex is shown in the all-down conformation. Its S1 and S2 subunits are depicted in red and blue We display the domains highlighted in the Spike structure , shown from two different perspectives ... S309 Fab binding to up-RBD was modeled by rigid-body alignment to closed-RBD and Fab interactions from PDB structure 6WPT (21), using the backbone of residues 331 to 527 for least squares fitting.
43 6wpt 7jvc, 7k43, 7k4n, 7jv6, 7jw0 Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies 2021 R Yan, R Wang, B Ju, J Yu, Y Zhang, N Liu, J Wang- Cell research, 2021 - nature.com Neutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus disease 2019 (COVID-19). We isolated a large number of nAbs from SARS-CoV-2-infected ... Besides, there are some special antibodies that can compete ACE2 binding while bind to RBD with different patterns. We assigned these antibodies into class IV which contains S309 (PDB code: 6WPT), C110 (PDB code: 7K8V) and C135 (PDB code
44 4lgv - Structural basis for substrate recognition of glucose-6-phosphate dehydrogenase from Kluyveromyces lactis 2021 HH Vu, C Jin, JH Chang- Biochemical and Biophysical Research, 2021 - Elsevier The overall structure of Kluyveromyces lactis G6PD (cyan), Homo sapiens G6PD ( PDB code, 2BHL; red), Trypanosoma cruzi code, 6D23; yellow), Leuconostoc mesenteroides G6PD ( PDB code, 1DPG; purple), and Mycobacterium avium G6PD ( PDB code, 4LGV ; green)
45 4jv3 4f32 Semisynthesis and Biological Evaluation of Platencin Thioether Derivatives: Dual FabF and FabH Inhibitors against MRSA 2021 Y Li, X Weng, Y Deng, J Pan, S Zhu- ACS medicinal, 2021 - ACS Publications The discovery and clinical use of multitarget monotherapeutic antibiotics is regarded as a promising approach to reduce the development of antibiotic resistance. Platencin (PTN), a potent natural a... On the basis of the X-ray structures of PTN with ecFabF(C163Q), Burkholderia vietnamiensis FabF, and Brucella melitensis FabB (PDB IDs 3HO2, 4F32, and 4JV3, respectively) as well as that of platencin A1 with ecFabF-(C163Q) (PDB ID 3HO9), it is likely that these PTN derivatives may also interact with FabF or
46 4o5o - A fragment-based protein interface design algorithm for symmetric assemblies 2021 J Laniado, K Meador, TO Yeates- Protein Engineering, Design, 2021 - academic.oup.com The expansive database of known protein structures provides valuable empirical frameworks for The growing focus on secondary structure associations motivates an attempt to bring by precomputing common proteinprotein fragment configurations from known structural data
47 3tcq - Targeting ebola virus VP40 protein through novel inhibitors: exploring the structural and dynamic perspectives on molecular landscapes 2021 S Khan, Z Fakhar, A Ahmad- Journal of Molecular Modeling, 2021 - Springer of novel antiviral drugs. Computational methods. Structural modelling. The X-ray crystallographic structure of VP40 protein ( PDB Code: 3TCQ ) [12] was retrieved from the Protein Data Bank (www.rcsb.org). The structure was prepared
48 6x79 - A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features 2021 S Fatihi, S Rathore, A Pathak, D Gahlot, M Mukerji- bioRxiv, 2021 - biorxiv.org Cryo-EM structures of the D614G spike structure have revealed that the mutant D614 is stable with RBD in an up mational states of the spike were analysed (see Methods for PDB ids) spike conformers showed large structural changes, with an average deviation of 2.77 0.42 ... 18 cryo-EM structures for closed spike conformation (PDB ID: 6ZGE, 6VXX, 6X2C, 6X6P, 6X29, 6X79, 6XF5, 6XLU, 6XM5, 6ZB4, 6ZB5, 6ZGI, 6ZP0, 7CAB, 7DDD, 7DF3, 7JJI and 7JWY) were taken from RCSB P
49 4wgj 4xi8, 4py3, 4lu4 Fic and non-Fic AMPylases: protein AMPylation in metazoans 2021 BK Chatterjee, MC Truttmann- Open Biology, 2021 - royalsocietypublishing.org name, organism name, references, function/targets, structure ( PDB ID) BepC, Bartonella henselae, [59], triggers actin stress fibre formation in HeLa cells, 4WGJ salt bridges occur between (a) Asp117 and Lys119 of the extended flap region (a -hairpin like structure that partially
50 6vxx - RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental 2021 SK Burley, C Bhikadiya, C Bi, S Bittrich- Nucleic acids, 2021 - academic.oup.com Biology; Nucleic Acid Enzymes; RNA and RNA-protein complexes; Structural Biology; Synthetic Biology and Bioengineering; Methods Online; Surveys and Summaries; Database; Web Server. Advance articles; Submit: Author Guidelines;
51 4mei 4kz1, 4nhf, 4lso, 4jf8, 4o3v Structural and Biochemical Analysis of OrfG: The VirB8-like Component of the Conjugative Type IV Secretion System of ICESt3 From Streptococcus 2021 J Cappele, A Mohamad Ali- Frontiers in molecular, 2021 - frontiersin.org The first step of structure comparison was conducted with both DALI (Holm and Sander, 1995) and and Henrick, 2004) to fetch a complete list of VirB8 structures (26 PDB entries 16 structures was conserved (2cc3, 3ub1, 3wz3, 3wz4, 4akz, 4ec6, 4jf8, 4kz1, 4lso, 4mei , 4nhf, 4o3v
52 6tys - Study of Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal-X) of Monoclonal mice/human antibodies 2021 IV Ferrari, P Patrizio- bioRxiv, 2021 - biorxiv.org zone between 150-210 residues amino acids; with the exception of ID PDB 3I9G-3W9D 6TYS : (A potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits Nipah virus and Antibodies all have the same basic structure consisting of two heavy and two light
53 6mg6 - Genome Mining, Phylogenetic and Structural Analysis of Bacterial Nitrilases for the Biodegradation of Nitrile Compounds 2021 R Salwan, V Sharma, S Das - 2021 - researchsquare.com ( PDB :1EMS), Helicobacter pylori ( PDB : 6MG6 ), Mus musculus ( PDB : 2W1V), Pyrococcus abyssi ( PDB : 3WUY) has already been reported. However, with most of the nitrilases, the crystal structure had been resolved, came
54 6ws6 - CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro 2021 MT Ma, S Badeti, CH Chen, J Kim- Frontiers in, 2021 - frontiersin.org Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is highly contagious and presents a significant public health issue. Current therapies used to treat coronavirus disease 2019 (COVID-19) include monoclonal antibody cocktail, convalescent plasma, antivirals ... Plasmid construct of S309-CAR. The SFG retroviral vector contains the S309 single chain antibody fragment (accession code 6WS6 on PDB)
55 5k0s - Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium 2021 GF Mercaldi, M de Oliveira Andrade- Journal of Biological, 2021 - ASBMB In addition, XcMetRS was compared with MetRS1 enzymes in complex with dual-site inhibitors from Trypanosoma brucei (PDB code: 4EGA) (48, 67), Brucella melitensis (PDB code: 5K0S) (35, 68), and S. aureus (PDB code: 4QRD)
56 6nb7 6nb6 Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein Through Molecular Dynamics Simulation 2021 Y Li, T Wang, J Zhang, B Shao, H Gong- arXiv preprint arXiv, 2021 - arxiv.org taking the S proteins of SARS-CoV with 2 upward RBDs ( PDB ID: 6NB6) (21) and 3 upward RBDs ( PDB ID: 6NB7 ) (21) as We also conducted a time- structure based Independent Components Analysis (tICA) (34, 35) to identify slow motions with high time autocorrelation on
57 4f4h 5kha, 6mg6 Crystal Structure of Nitrilase-Like Protein Nit2 from Kluyveromyces lactis 2021 C Jin, H Jin, BC Jeong, DH Cho, HS Chun, WK Kim- Crystals, 2021 - mdpi.com On Novel Copper Based Alloys Development via Friction Stir Alloying... The corresponding C-terminal region is shown in red. The six homologous structures indicate the following: BtGlu-dep_NAD+ synthetase: glutamine dependent NAD+ synthetase from Burkholderia thailandensis (PDB code, 4F4H). .. The two homologous structures indicate the following: HpCN hydrolase: CN hydrolase from Helicobacter pylori (PDB code, 6MG6)
58 4nbr - PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations 2021 F Adasme-Carreno, J Caballero- Journal of Chemical, 2021 - ACS Publications Inf. Model. 2021, 61, 4, 1789-1800. ADVERTISEMENT. RETURN TO ISSUEPREVComputational Chemis...Computational ChemistryNEXT. Journal Logo. PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations
59 3tmg 4f3p, 4z9n Gating the channel pore of ionotropic glutamate receptors with bacterial substrate binding proteins 2021 M Bernhard, B Laube- bioRxiv, 2021 - biorxiv.org The bacterial GluR0 receptor was chosen due to its less complex architecture compared to eukaryotic iGluRs, characterized by the lack of an NTD, a Therefore, we used the structure of the glutamate-bound closed GluR0-LBD conformation (Mayer et al., 2001) ( PDB ID
60 5koi - Bufotenine and its derivatives: synthesis, analgesic effects identification and computational target prediction 2021 Z Chao, C Min, SUN Shan-Liang, W Jiao-Jiao- Chinese Journal of, 2021 - Elsevier Class Target PDBa Glideb MMGBSA Class Target PDB Glide MMGBSA Class Target PDB Glide MMGBSA mGLuR5 4OO9 0.52 37.15 GLP1 3IOL 4.50 23.75 NaV1.7 5KOI 2.85 25.53 silver chlor- ide is added for substitution to obtain a stable structure of compound 6 with
61 6nb3 - Origen del SARS-CoV-2 desde una perspectiva Bioinformtica 2021 R Isea- Conocimiento Libre y Licenciamiento (CLIC), 2021 - convite.cenditel.gob.ve 6NB3 1359 MERS-CoV secuencias de la glicoprotena de espcula S que han sido recopiladas en la base de datos de protenas PDB Sequence analysis and structure predition of SARS-CoV-2 accesory proteins 9b and ORF14: evolutionary analysis indicates close
62 6ns0 - Synthesis of erythrodiol C-ring derivatives and their activity against Chlamydia trachomatis 2021 O Kazakova, L Rubanik, A Lobov, N Poleshchuk- Steroids, 2021 - Elsevier activity, for example, the presence of ,-unsaturated system in the structure of CDDO (2-cyano-3,12-diooxoolean-1,9-dien-28-oic acid) has a sufficient influence on anti-inflammatory, anti-diabetic nephropathy, and cytotoxic activities [14], [15] Figure 1. Structures of oleanolic
63 6cum - Introduction to molecular replacement: a time perspective 2021 E Dodson- Acta Crystallographica Section D: Structural, 2021 - Wiley Online Library the phase error between the correct value and the phases generated from the best solution; Dphi_DM, the phase error after density modification, which was performed with Parrot, except for PDB entry 6cum , which used Rebuilt?, Yes if the test structure could be rebuilt
64 6wsa 4ghk, 4rgb, 3sgw, 4w5k, 3kcq, 3oxk, 3ppi Principal component analysis of alpha-helix deformations in transmembrane proteins 2021 A Bevacqua, S Bakshi, Y Xia- PloS one, 2021 - journals.plos.org 6tt4, 6txw, 6tzj, 6uqw, 6v47, 6vbj, 6vie, 6vjd, 6vmz, 6vnw, 6w1w, 6w2x, 6wok, 6wsa , 6x1q, 6x2m and the contribution of each physical deformation to the overall flexibility of the secondary structure N -helices of a given length (L residues) were collected from PDB entries (See
65 6q06 - Cryptic SARS-CoV2-spike-with-sugar interactions revealed by'universal'saturation transfer analysis 2021 CJ Buchanan, B Gaunt, PJ Harrison, A Le Bas, A Khan- bioRxiv, 2021 - biorxiv.org computational modelling environments provide exact structural models. In this way, uSTA analysis provides an automated pipeline from raw NMR free induction decay (FID) signals all the way to proteinligand structures in a freely available form for the non-expert
66 6wps - Modernized uniform representation of carbohydrate molecules in the Protein Data Bank 2021 C Shao, Z Feng, JD Westbrook, E Peisach- , 2021 - academic.oup.com glycan structures (eg, SARS-CoV-2 protein-carbohydrate complex PDB ID 6WPS ) and the partnership is committed to maintaining consistency and accuracy across the PDB archive by regularly reviewing data processing procedures and carrying out structure remediation efforts
67 5viu - Identification and expression profiling of proline metabolizing genes in Arabidopsis thaliana and Oryza sativa to reveal their stress-specific transcript alteration 2021 S Arabia, MNA Shah, AA Sami, A Ghosh- Physiology and Molecular, 2021 - Springer 2020) to stabilize the intracellular environment as well as the structures of proteins, membranes, and subcellular organelles (Verslues et al Data retrieval from Arabidopsis and Rice genome databases, and construction of gene structure and domain architecture
68 6x79 - Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS CoV-2 2021 RC Penner- BioRxiv, 2021 - biorxiv.org E of rotations of BHBs in HQ60; Table 1, Protein Data Bank structure files upon The methods of this paper are im- plented online from an uploaded PDB file at et al., Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture , Nature Communications, 5
69 6tz8 - Uneditedversion published onlineon 15/7/2021 2021 G Biswas, R Banerjee - currentscience.ac.in exclusively with P2, while P1 mediates molecular recognition and binding, as evident from the crystal structures of (truncated) SurA-peptide complexes46 The crystal structure of CaEss1 showed structural similarity to the human PIN1 protein except for the
70 5vn4 - Acyclic nucleoside phosphonates with adenine nucleobase inhibit Trypanosoma brucei adenine phosphoribosyltransferase in vitro 2021 E Doleelov, T Klejch, P paek, M Slapnikov- Scientific Reports, 2021 - nature.com Acyclic nucleoside phosphonates (ANPs) represent a group of compounds whose biological activity is based on their structural resemblance to the natural nucleotides 8,9 . Their flexibility enables them to adopt a conformation suitable for the interaction with the active site ... To assess the probable binding modes of the most potent inhibitors, docking calculations were performed. Since T. brucei APRT1 has been slightly explored so far, the only experimental structure that is available for this enzyme
71 4wbs - Structural modeling of the Treponema pallidum OMPeome: a roadmap for deconvolution of syphilis pathogenesis and development of a syphilis vaccine 2021 KL Hawley, JM Montezuma-Rusca- Journal of, 2021 - Am Soc Microbiol TP0786 Phyre2 LptB; Burkholderia phymatum; 4WBS 50 conserved in T. pallidum BamA, we performed structure -based sequence alignment of the 170 TP0326 3D model with the crystal structures of E. coli BamA ( PDB ID: 5D0Q, 5D0O) (60). The 171
72 4npc - Characterization of xylitol 4-dehydrogenase from Erwinia aphidicola and its co-expression with NADH oxidase in Bacillus subtilis 2021 M Li, W Zhu, Q Meng, M Miao, T Zhang- Process Biochemistry, 2021 - Elsevier XDH, EC 1.1.1.B19) catalyzes the interconversion of xylitol and l-xylulose [11], and its primary structure is highly Computer simulation and analysis facilitated the extraction of potential structural information, which may help us further investigate the catalytic mechanism of XDH ... and the crystal structure of sorbitol dehydrogenase from Brucella suis as a template (PDB ID: 4NPC). The quality of the model was evaluated using the SAVES server. Molecular docking was conducted using Autodock
73 5vcu - Interpretable Neural Networks based classifiers for categorical inputs 2021 S Zamuner, PDL Rios- arXiv preprint arXiv:2102.03202, 2021 - arxiv.org cartoon representation of RAS protein (green) bounded to GDP (light blue spheres) from pdb 5vcu belonging to the most relevant predicted triplets are clustered in the structure of the Note that, to better compare to plmDCA, the same architecture and hyperparameters have
74 6nb3 - Discovery of Small Molecule Entry Inhibitors Targeting the Fusion Peptide of SARS-CoV-2 Spike Protein 2021 X Hu, CZ Chen, M Xu, Z Hu, H Guo, Z Itkin- ACS Medicinal, 2021 - ACS Publications SARS-CoV-2 entry into host cells relies on the spike (S) protein binding to the human ACE2 receptor. In this study, we investigated the structural dynamics of the viral S protein at the fusion pept... Comparison of the FP binding pocket of the spike protein of SARS-CoV-2 (PDB 6XR8), SARS-CoV-1 (PDB 5WRG), and MERS (PDB 6NB3). The spike protein is rendered in ribbons with the FP colored in magenta and the HR1 domain in blue.
75 5tw7 - Discovery of Novel GMPS Inhibitors of Candidatus Liberibacter Asiaticus by Structure Based Design and Enzyme Kinetic 2021 J Nan, S Zhang, P Zhan, L Jiang- Biology, 2021 - mdpi.com SwissModel was employed to generate the three-dimensional structure of CLas GMPS using Neisseria gonorrhoeae GMPS ( PDB ID: 5TW7 ) as a The homology model of the CLas GMPS structure was a dimer (Figure 1). The quality of the three-dimensional structure of CLas
76 6wpt - Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane 2021 YK Choi, Y Cao, M Frank, H Woo, SJ Park- Journal of chemical, 2021 - ACS Publications The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2) and is considered the major target for drug and vaccine development. We previously built fully glycosylated full-length SARS-CoV-2 S protein models in a viral membrane ... In the cryo-EM structure of the S trimer in the complex with the S309 antibody (PDB ids: 6WPS and 6WPT(51)), S309 interacts with the glycan attached to N343.
77 4gl8 - Host-specific functional compartmentalization within the oligopeptide transporter during the Borrelia burgdorferi enzootic cycle 2021 AM Groshong, MA McLain, JD Radolf- PLoS pathogens, 2021 - journals.plos.org Structural homology models demonstrated variations within the binding pockets of OppA1, 2, and 5 indicative of different peptide repertoires We used larval immersion feeding [43] to confirm that oppA1 is essential for structural integrity of the spirochete during the blood meal
78 2lwk - Supporting Information for Occurrences of protonated base triples in RNA are determined by their cooperative binding energies and specific functional 2021 A Halder, A Jhunjhunwala, D Bhattacharyya, A Mitra - biorxiv.org Figure S1: Context of occurrences of G(CC) H:+ Trans/W:W Cis triple (System 2). 2D representation of (A) the 5S rRNA, (B) Domain III of 25S rRNA of S. cerevisiae and (C) HDV ribozyme are shown and the structural motifs that contain (G) 3D structure of the PDB : 3KIR Chain: A
79 5vbf - The tetrameric assembly of 2-aminomuconic acid dehydrogenase is a functional requirement of cofactor NAD+ binding 2021 Q Shi, Y Chen, X Li, H Dong, C Chen, Z Zhong, C Yang- bioRxiv, 2021 - biorxiv.org 144 The overall structure of AmnC protomers shares the general architecture of the ALDH 145 family (SSADH) ( PDB code:2W8P)(23-26). Pairwise superposition of the six protomers yielded 164 In this study, we elucidated the structure of AmnC and how it 260
80 6x79 - Structure-based design of a highly stable, covalently-linked SARS-CoV-2 spike trimer with improved structural properties and immunogenicity 2021 E Olmedillas, CJ Mann, W Peng, YT Wang, RD Avalos- bioRxiv, 2021 - biorxiv.org For VFLIP_D614G, a population of 213,852 particles yielded a 2.8 resolution structure (Figure S2). Importantly, the density maps confirm Further sub-classification revealed an overall architecture that is similar to other closed spikes in the Protein Data Bank ( PDB ). ... A previously published structure of the SARS-CoV-2 ectodomain with all RBDs in the down conformation (PDB ID 6X79) was used to fit the cryo-EM maps in UCSF ChimeraX
81 5udf - Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria 2021 I Alav, J Kobylka, MS Kuth, KM Pos, M Picard- Chemical, 2021 - ACS Publications Journal Logo. Structure , Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Ilyas Alav Ilyas Alav. Institute of Microbiology and Infection, College of Medical and Dental Sciences
82 4kzp - Enzymatic -Oxidation of the Cholesterol Side Chain in Mycobacterium tuberculosis Bifurcates Stereospecifically at Hydration of 3-Oxo-cholest-4,22-dien-24-oyl-CoA 2021 T Yuan, JM Werman, X Yin, M Yang- ACS Infectious, 2021 - ACS Publications The unique ability of Mycobacterium tuberculosis (Mtb) to utilize host lipids such as cholesterol for survival, persistence, and virulence has made the metabolic pathway of cholesterol an area of great interest for therapeutics development. Herein, we identify and characterize two genes from the Cho-region (... A search model for the apo-protein was created from 4KZP and the holo-protein model was created from the ChsB1 apo-protein model.
83 5udf - Structural basis for bacterial lipoprotein relocation by the transporter LolCDE 2021 X Tang, S Chang, K Zhang, Q Luo, Z Zhang- Nature Structural &, 2021 - nature.com Advertisement. Advertisement. Nature Structural & Molecular Biology. View all journals; Search; My Account Login. Explore content; Journal information; Publish with us Structural basis for bacterial lipoprotein relocation by the transporter LolCDE
84 6bfu - Insight into Vaccine Development for Alphacoronaviruses Based on Structural and Immunological Analyses of Spike Proteins 2021 Y Shi, J Shi, L Sun, Y Tan, G Wang, F Guo- Journal of, 2021 - Am Soc Microbiol (B) Overall structure comparison of coronavirus S-trimers. The S-trimer structures of HCoV-229E ( PDB ID: 6U7H), HCoV-NL63 ( PDB ID: 5SZS), PEDV ( PDB ID: 6U7K), FIPV ( PDB ID: 6JX7), PDCoV ( PDB ID: 6BFU ), IBV ( PDB ID: 6CV0), SARS-CoV ( PDB ID: 5X5B), SARS
85 5i4m - Zn2+-dependent enhancement of Atrazine biodegradation by Klebsiella variicola FH-1 2021 J Zhang, X Wu, X Zhang, H Pan, JES Shearer- Journal of Hazardous, 2021 - Elsevier chloromuconate to generate maleylacetate (Cmara et al., 2008). As a major structural component in the cell wall, peptidoglycan plays important roles in cell growth. Studies have shown that three zinc-dependent endopeptidases
86 6wps 7jvc, 7k43, 7jv2, 7jxe, 7jw0 Structural analysis of neutralizing epitopes of the SARS-CoV-2 spike to guide therapy and vaccine design strategies 2021 MT Finkelstein, AG Mermelstein, E Parker Miller- Viruses, 2021 - mdpi.com Multiple structures of S in complex with ACE2 have been determined [9,17,21,22,26 S proteins from SARS-CoV, SARS-CoV-2, and MERS-CoV undergo dramatic structural changes to S2 forms an elongated structure , and the two heptad repeats, HR1 and HR2, eventually form a ... S2M11 from RBM Class III (PDB ID 7K43 [71]), and CR3022 (left) and S309 (right) from RBD Core (PDB IDs 6W41 [86] and PDB ID 6WPS [
87 4ix8 - Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies 2021 D Suplatov, Y Sharapova, V vedas- Multiple Sequence Alignment, 2021 - Springer etc.): 3WGB, 2W7E, 3A2B, 1IBJ, 1LKC, 1 V72, 2BKW, 2EZ2, 4IX8 , 1QZ9, 4BA5 The missing loop regions in these PDB structures were reconstructed using the MODELLER software [23] enzymes, the MATT algorithm was used to prepare the initial 3D- structure superimposition of -- This is not a duplicate of their earlier 2018 work
88 6vyb - Ethnomedicines of Indian origin for combating COVID-19 infection by hampering the viral replication: using structure-based drug discovery approach 2021 S Alagu Lakshmi, RMB Shafreen, A Priya- Structure and, 2021 - Taylor & Francis CoV-2 main protease ( PDB ID: 5R82. pdb ), spike protein ( PDB ID: 6VYB . pdb ) and human In order to minimize the energy, PDB structures of the target proteins were refined through for combating COVID-19 infection by hampering the viral replication: using structure -based drug
89 3qh4 - Structure guided engineering of a cold active esterase expands substrate range though a stabilisation mutation that allows access to a buried water chamber 2021 N Noby, R Johnson, J Tyzack, A Embaby, H Saeed- bioRxiv, 2021 - biorxiv.org to fully open the HerE plug. LipW ( PDB 3QH4 ) (26) has two shorter residues in place PestE ( PDB 2YH2) (28) does not have the plug (Figure 2b). N211 is replaced by a of helical character than the WT suggesting a higher degree of structure for the mutant at this temperature
90 6vxx 6vyb Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations 2021 K Akisawa, R Hatada, K Okuwaki, Y Mochizuki- RSC Advances, 2021 - pubs.rsc.org Here, we report on interaction analyses of the spike protein in both closed ( PDB -ID: 6VXX ) and open interaction energies were evaluated for both structures , and a mutual comparison indicated considerable losses of stabilization energies in the open structure , especially in
91 6q04 - Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity 2021 D Pal- Journal of Structural Biology, 2021 - Elsevier The structural and dynamics analyses of the Spike show that its fusion loop spatially organizes three fusion peptides contiguous to each other to synergistically I propose a Contact Initiation Model based on the architecture of the Spike quaternary structure that explains the
92 4qji - Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site 2021 V Mendes, SR Green, JC Evans, J Hess- Nature, 2021 - nature.com Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis
93 4dz4 - Structure of the E. coli agmatinase, SPEB 2021 I Chitrakar, SF Ahmed, AT Torelli, JB French- Plos one, 2021 - journals.plos.org The first stage used the default parameters with the structure of Burkholderia thailandensis hypothetical agmatinase ( 4DZ4 ) [34] as To place the ligand in the SPEB active site, the structure of the D. radiodurans agmatinase with bound hexane-1,6-diamine ( PDB code 1WOG
94 5ha4 - In silico prediction, molecular docking and binding studies of acetaminophen and dexamethasone to Enterococcus faecalis diaminopimelate epimerase 2021 H Singh, S Das, J Yadav, VK Srivastava- Journal of Molecular, 2021 - Wiley Online Library are also available in the PDB , but are to date otherwise unpublished, including Acinetobacter baumannii ( PDB : 5HA4 ), Bacillus anthracis ( PDB : 2OTN structural and functional studies of DAP epimerase from different organisms have reported that the structure consists of
95 3o2e - Phosphorylation status of BolA affects its role in transcription and biofilm development 2021 L Galego, S Barahona, CV Romo- The FEBS, 2021 - Wiley Online Library NMR structure of mouse BolA1 ( PDB ID 1V60) and E. coli BolA ( PDB ID 2DHM) reveal a structure with similarity to nucleic acid binding proteins including a helix-turn [6]. MreB is a structural homologue of actin that is essential for cell elongation, maintenance of
96 6x79 7jv2 Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors 2021 Baysal, N Abdul Ghafoor, RS Silme, AN Ignatov- PloS one, 2021 - journals.plos.org The 3' end of the genome encodes 4 major structural proteins, including the spike protein (S), the nucleocapsid protein structure of refusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation ( PDB : 6X79 ), and X-ray diffraction structure of SARS
97 6nb6 - Review of COVID-19 antibody therapies 2021 J Chen, K Gao, R Wang, DD Nguyen- Annual review of, 2021 - annualreviews.org S230 SARS-CoV RBD IgG = 0.06 / BLI (73) 6NB6 (73) 4.30 Three-Dimensional Structure Alignment All of the available 3D structures of the SARS-CoV-2 S-protein RBD in complex with antibod- ies are aligned to ACE2 The PDB ID of these complexes can be found in Table 1
98 6q09 - Diversity of structures and functions of oxo-bridged non-heme diiron proteins 2021 MLC Nogueira, AJ Pastore, VL Davidson- Archives of Biochemistry and, 2021 - Elsevier Archives of Biochemistry and Biophysics. Diversity of structures and functions of oxo-bridged non-heme diiron proteins. ... Fig. 3. Examples of the different combinations of amino acid residues that coordinate the irons in hemerythrin-like proteins. A. HLP from Mycobacterium kansasii with 4H/2E/1Y coordination (PDB entry 6Q09)
99 6q07 - In-Silico evidence for a two receptor based strategy of SARS-CoV-2 2021 E Milanetti, M Miotto, L Di Rienzo- Frontiers in molecular, 2021 - ncbi.nlm.nih.gov Complex between MERS spike protein and sialic acid: PDB code 6Q07 Unbound SARS-CoV spike protein: PDB code 6CRV We use DMS (Richards, 1977) to compute the solvent accessible surface for all proteins structure , given their x-ray structure in PDB format (Berman et al
100 4kzk - Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus 2021 JE Bae, IJ Kim, Y Xu, KH Nam- The protein journal, 2021 - Springer of RmSBP, we performed comparative analysis and substrate docking studies using a previously reported crystal structure of SBP ( PDB code 5Z6V) as the initial model structure Among them, 9 models ( PDB codes: 3LFT, 2QH8, 5ER3, 4RS3, 4KZK , 5BRA, 3KSM, 2DRI
101 6w7x - Biochemical Characterization and Structural Analysis of N-acetylornithine Transaminase from Synechocystis sp. PCC6803 2021 F BAI, Z LI, X WANG, Z HU, L BAO- Biotechnology, 2021 - biotech.aiijournal.com PLP PLP slr1022, 2E54, 6W7X , 2EH6 and SWISS- MODEL N- PDB ID 2E54 A: Cartoon structure of Slr1022
102 6wpt - Synthesis and cytotoxic activity of novel Indole derivatives and their in silico screening on spike glycoprotein of SARS-CoV-2 2021 P Gobinath, DA Ponnusamy Packialakshmi- Frontiers in molecular, 2021 - ncbi.nlm.nih.gov molecular protein crystal structure of spike glycoprotein of SARS-CoV-2 PDB ID 6WPT The ligand preparation module optimized the ligand 3D structure of selected molecules to remove molecular interaction analysis with selected small molecules of (1c) with 6WPT protein was
103 4f2n 4f40 DOCKING MOLECULAR E AVALIAO DA ATIVIDADE ANTILEISHMANIA IN VITRO DE UM COMPLEXO METLICO DE RUTNIO COM EPIISOPILOTURINA E 2021 J Arajo- -Revista Cientfica Multidisciplinar-ISSN 2675-6218, 2021 - recima21.com.br The 3D protein structures of L. major targets were obtained from the Protein Data Bank ( PDB ) database with codes 1e7w (Pteridine reductase), 5nzg (UDP-glucose Pyrophosphorylase), 5g20 (Glycyl Peptide N-tetradecanoyltransferase), 5c7p Enzimas Identificao PDB 4F2N
104 3ujh - Engineering of the cytosolic form of phosphoglucose isomerase into chloroplasts improves plant photosynthesis and biomass 2021 F Gao, H Zhang, W Zhang, N Wang, S Zhang- New, 2021 - Wiley Online Library in Shanghai, China. Diffraction data were processed by HKL2000 and the PGIs structure models ( PDB : 3UJH ). After cycles of auto model building (PHENIX) (Liebschner et al., 2019) and To investigate the structural basis for the dramatic activity difference between TaPGIc and
105 6bfu - Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins 2021 Y Shi, J Shi, L Sun, Y Tan, G Wang, F Guo- Journal of, 2021 - Am Soc Microbiol recognition pattern, especially the structure of the RBD and its state in the S-trimer, 112 Structural and immunological analyses of alpha- and beta-coronaviruses spike 124 proteins 125 To date, multiple S-trimer structures of coronaviruses have been resolved (12-14, 126
106 6cw5 - In silico Structural Modelling of Ribokinase from Salmonella Typhi 2021 H Abubakar, Y Ndatsu, AD Musa, C Ogbiko- Earthline Journal of, 2021 - ubipayroll.com done to check the stereochemical features of the predicted 3-dimensional structure of the BLASTp showed low identity of 40% (Table 1) with other proteins deposited in PDB and conserved domain (Figure 1). Multiple sequence alignment between the query, 6CW5 , 2FV7, 1VM7
107 6wgy 3hwk Structural basis of the cooperative activation of type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554 2021 SH Park, CW Lee, DW Bae, H Do, CS Jeong- International Journal of, 2021 - Elsevier of citrate-bound HyCS (closed conformation) and apo-EcCS (open conformation, PDB code: 4G6B residues showed a face-to-edge interaction in the open state structure of EcCS citrate binding-induced conformational changes result in the transfer of further structural changes to ... Mycobacterium tuberculosis (PDB code 3HWK), has a Lys residue at the position corresponding to Trp262 of HyCS but that from the Mycobacterium tuberculosis variant bovis AF2122/97 (PDB code 6WGY) contains a Ser residue instead
108 5bq2 - The Mur Enzymes Chink in the Armour of Mycobacterium tuberculosis Cell Wall 2021 Y Shinde, I Ahmad, S Surana, H Patel- European Journal of Medicinal, 2021 - Elsevier Mtb Mur ligases with the same catalytic mechanism share conserved amino acid regions and structural features that can conceivably exploit for the designing of the inhibitors, which can simultaneously target more than one isoforms (MurC-MurF) of the enzyme ... According to sequence homol- ogy search using BLASTp against PBD, 06 proteins structure tem- plates (PDB ID 3SG1, 5BQ2, 3ISS, 1A2N, 1UAE, and 3R38) were picked based on sequence identity and more statistical significance,
109 6nbo - Purification, characterization, and catalytic mechanism of N-Isopropylammelide isopropylaminohydrolase (AtzC) involved in the degradation of s-triazine 2021 N Zhou, J Wang, W Wang, X Wu- Environmental Pollution, 2021 - Elsevier The structural architecture of AtzC resembled that of cytosine deaminase in class III Purification and structural characterization of AtzE produced by the model bacterium Pseudomonas sp and substrate specificity of AtzC were studied, and the function, structure , and evolutionary
110 4ziy - Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening 2021 M Kumari, N Subbarao- Journal of Biomolecular Structure and, 2021 - Taylor & Francis extracted eight protein templates: 1GG4, 2AM1, 3ZM5, 4CVK, 4QDI, 4QDI, 4QF5 and 4ZIY , which identity best model with the low RMS value of superposition using Swiss- pdb viewer (Guex The modeled 3D structure of Mur enzymes showed close similarity to 3D crystal protein
111 6q04 - Transformations, Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B. 1.1. 7 2021 O Basidas, D Kokron, CE Henze- bioRxiv, 2021 - biorxiv.org Clustal Omega uses a structure guided hidden Markov model (HMM) for multiple sequence alignment. Sequences were obtained directly from the PDB files across four different corona viruses SARS-CoV (6ACD) [14], SARS-CoV-2 (6VSB) [10], MERS-CoV ( 6Q04 ) [20], and
112 6x79 - Chitosan derivatives: A suggestive evaluation for novel inhibitor discovery against wild type and variants of SARS-CoV-2 virus 2021 C Modak, A Jha, N Sharma, A Kumar- International Journal of Biological, 2021 - Elsevier of efficacious treatment strategies to robustly tackle this pandemic by targeting various pathways and mechanisms of infection by either creating new drug molecules or repurpose already existing drug molecules for impacting virus infection cycle or structural proteins [2] ... For heparan sulfate proteoglycan/heparin-binding site as target site, the homotrimerectodomain in prefusion state of S-glycoprotein PDB ID: 6X79 with a low resolution of 2.90 Å was considered
113 6ok4 4k9d, 4lsm Structure determination and analyses of the GAPDH from the parasite Schistosoma mansoni, the first one from a platyhelminth 2021 S Boreiko, M Silva, J Iulek- Biochimie, 2021 - Elsevier The GAPDH’s structures selected for sequence alignment were from: Brugia malayi, Bmal - PDB ID: 4K9D ... and Chlamydia trachomatis, Ctra - PDB ID: 6OK4 [66]
114 6xdh - A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico 2021 A Rakib, Z Nain, SA Sami, S Mahmud- Briefings in, 2021 - academic.oup.com Abstract. Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declar. ... For docking analysis, the following receptors were selected: PDB ID 6M3M for N protein, PDB ID 2GHV for the RBD of the S protein, PDB ID 6W9C for PLpro, PDB ID 6 M71 for RdRp, PDB ID 6ZSL for SARS-CoV-2 helicase (nsp13), 6WC1 for nsp9 RNA-replicase, and 6XDH for nsp15
115 5vp5 3enn Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases 2021 EM Cross, FG Adams, JK Waters, D Arago- Scientific reports, 2021 - nature.com Treatments for 'superbug' infections are the focus for innovative research, as drug resistance threatens human health and medical practices globally. In particular, Acinetobacter baumannii (Ab) infections are repeatedly reported as difficult to treat due to increasing antibiotic resistance
116 4yet 3js4 Amide- interactions in active centers of superoxide dismutase 2021 S Stojanovi, ZZ Petrovi- Journal of the Serbian, 2021 - doiserbia.nb.rs A, 3js4:A, 3lio:A, 3lsu:A, 3mds:A, 3pu7:A, 3tqj:A, 4br6:A, 4c7u:A, 4f2n:A, 4ffk:A, 4yet :A, 5a9g 7. Example of the structure preferred amide interactions of FeSOD from the Thermosynechococcus elongatus ( PDB code 1my6): (a) parallel-displaced and (b) T-shaped structure
117 6brl - Metabolic impact of pathogenic variants in the mitochondrial glutamyltRNA synthetase EARS2 2021 M Ni, LF Black, C Pan, H Vu, J Pei, B Ko- Journal of Inherited, 2021 - Wiley Online Library 3A and B). Structural modeling of human EARS2 was obtained from the SWISS-MODEL Page 10. repository (Bienert et al 2017) based on the crystal structure of the glutamyl-tRNA synthetase from Elizabethkingia meningosepticum ( PDB : 6brl ), and superimposed on the crystal
118 3rrp - Characterization of class II fumarase from Schistosoma mansoni provides the molecular basis for selective inhibition 2021 IA Cardoso, AKL de Souza, AMG Burgess- International Journal of, 2021 - Elsevier Highlights. The first SmFH II structure in complex with L-malate was determined at 1.85 resolution. Only two other class II structures with L-malate in active site are reported (M. tuberculosis fumarase - PDB code: 4ADL [34] and M. abscessus fumarase - PDB code: 3RRP [51]). All of them share the same close protein-ligand contacts with the equivalent amino acid residues,
119 6wps - CoV3D: a database of high resolution coronavirus protein structures 2021 R Gowthaman, JD Guest, R Yin- Nucleic acids, 2021 - academic.oup.com (A) Visualization of the superposed spike RBD complexes with antibody S309 ( PDB code 6WPS ) ( 20 ) and (B) A trimeric spike structure in RBD-closed conformation ( 5 ) ( PDB code 6VXX Park YJ, Tortorici MA, Wall A., McGuire AT and Veesler D. (2020) Structure , Function, and
120 6nb3 - What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2 2021 V Fedorov, E Kholina, S Khruschev, I Kovalenko- Viruses, 2021 - mdpi.com M-protein defines the shape of the viral envelope organizing CoVs assembly in the interaction with all other major structural proteins [9 Computational virology tools contribute greatly to the understanding of viral structure , infectivity and pathogenesis, and design of antiviral drugs ... The models of S-proteins of SARS-CoV and MERS-CoV were based on cryo-EM structures from the Protein Data Bank (PDB) with IDs 6NB3 and 5X58, respectively.
121 5ji5 - Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches 2021 G Selvaraj, S Kaliamurthi, GH Peslherbe- F1000Research, 2021 - ncbi.nlm.nih.gov Structural modeling approach to study host-SARS-CoV-2 proteins interaction and drug and similarity and with the highest resolution template automatically from PDB and then Then, the corresponding structures constructed by superimposing the modeled protein structure on to
122 4g6c - New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs 2020 H Okella, JJ Georrge, S Ochwo, C Ndekezi- Frontiers in, 2020 - ncbi.nlm.nih.gov a global docking procedure in four folds, motif-based prediction based on peptide conformation, rigid-body docking, scoring based on structural clustering; and final structure minimization. ... The affinity of peptide-motifs A15_B and A15_E was highest within chains of the target proteins (PDB ID 1rrv, 4g6c, and 4oj8).
123 6nb6 6q05, 6nb8, 6nb7 Drug targets for corona virus: A systematic review 2020 M Prajapat, P Sarma, N Shekhar, P Avti- Indian journal of, 2020 - ncbi.nlm.nih.gov inhibition property.[39] The structure (protein data bank [ PDB ] ID 5ZUV and 5ZVM) shows a stable 6-helix bundle structure with S230 antibody Fab fragment binds to the SARS-CoV complex to neutralize it, and their structures are also available ( PDB IDs: 6NB6 , 6NB7, and
124 6c87 - In silico and in vitro comparison of nicotinamide adenine dinucleotide phosphate dependent xylose reductase rossmaan fold in Debaryomycetaceae yeast family 2020 N Arumugam, T Boobalan, S Saravanan- Biocatalysis and, 2020 - Elsevier it is the Integrated examinations of protein structure assessment online tool ID, Organism, Aa length, Rossmann fold region, Range, Identified PDB template, Hydrogen 3, MH286916, M. caribbica, 359, DFIDVVIVGAGFTKAVAAALLGVPGAGFVAVYDG, 330359, 6C87 , L20, A17, V16
125 6nb8 - Use of Isoelectric Point for Fast Identification of Anti-SARS CoV-2 Coronavirus Proteins 2020 K Mallik - 2020 - preprints.org If we follow the radial structure of the SARS CoV-2 virion, a gradual fall the in the pI values is 6NB8 (+) Human S230 antigen-binding fragment light chain 6.046 to make anti-viral drugs for SARS CoV-2. From the pI consideration, application of human Interferon- ( PDB ID 1AU1
126 4ohc - Orotato fosforribosiltransferasa. Pasado, presente y futuro en el estudio estructural de las protenas. 2020 L Gonzlez-Segura, EI Carrizosa-Carbajal - bq.facmed.unam.mx Past, present and future in the structural study of proteins Key words: Phosphoribosyltransferase; three- dimensional structure ; conformational change; inhibition; pyrimidines synthesis str (PDBs 3M3H y 4RV4), de Burkholderia cenocepacia ( PDB 4OHC ), de Corynebacterium
127 3p3a 3hzu, 4lw8 Challenges and opportunities of automated proteinprotein docking: HDOCK server versus human predictions in CAPRI Rounds 3846 2020 Y Yan, J He, Y Feng, P Lin, H Tao- Proteins: Structure, 2020 - Wiley Online Library prediction of this dimer interface is expected. For T144, the TPC1 channel structures of mouse ( PDB ID: 6C9A) and Arabidopsis thaliana ( PDB ID: 5DQQ) were used as the templates to construct the human TPC2 channel structure ( PDB ID: 6NQ0). Despite the low sequence
128 4dz4 - Insights into the Mn2+ Binding Site in the Agmatinase-Like Protein (ALP): A Critical Enzyme for the Regulation of Agmatine Levels in Mammals 2020 MB Reyes, J Martnez-Oyanedel, C Navarrete- International Journal of, 2020 - mdpi.com Using comparative modeling we generated a structural model of LIM-ALP, including the Mn 2+ binding site, but without considering the first presents the general folding of this protein family, presenting only differences in the length of some of the secondary structure elements
129 6wps - Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies 2020 CO Barnes, CA Jette, ME Abernathy, KMA Dam- bioRxiv, 2020 - ncbi.nlm.nih.gov 1g) that were isolated from the same donor 5 . They share structural similarities with each other and with other VH353/short 1) and C144 Fab (from C144-S structure ) aligned on a RBD monomer. ACE2 ( PDB 6M0J; light green surface) is aligned on the same RBD for reference ... Composite model of C135-RBD (blue and gray, respectively) overlaid with the SARS-CoV-2 NAb S309 (sand, PDB 6WPS) and soluble ACE2
130 5cy4 - Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA 2020 M Szewczyk, D Malik, LS Borowski- Nucleic acids, 2020 - academic.oup.com Here, we report comprehensive functional, biochemical, and structural studies to elucidate REXO2 function in human mitochondria We also demonstrate that REXO2 degrades RNA in a structure - and sequence-dependent manner. ... The model that was used for molecular replacement was oligoribonuclease from Acinetobacter baumnii (PDB ID: 5CY4, Seattle Structure Genomics Centre for Infectious Diseases), which shares 48.3% sequence identity with REXO2.
131 6x79 - Characterization of the SARS-CoV-2 S protein: biophysical, biochemical, structural, and antigenic analysis 2020 NG Herrera, NC Morano, A Celikgil, GI Georgiev- ACS, 2020 - ACS Publications need to produce large quantities of high-quality SARS-CoV-2 Spike (S) protein for use in both clinical and basic science settings. To address this need, we have evaluated the expression and purification of two previously reported S protein constructs in Expi293F and ExpiCHO-S cells... In nine structures that align well in this region (conformation 1: 6VXX, 6X29, 6X2C, 6X79, 6ZOX, 6ZOY, 6ZP0, 6ZP1, 6ZWV), the amino acid segment 621–640 was not modeled, presumably due to disorder
132 4g50 3uqb Targeting Protein Folding: A Novel Approach for the Treatment of Pathogenic Bacteria 2020 NJ Scheuplein, NM Bzdyl, EA Kibble- Journal of Medicinal, 2020 - ACS Publications Infectious diseases are a major cause of morbidity and mortality worldwide, exacerbated by increasing antibiotic resistance in many bacterial species. The development of drugs with new modes of act...
133 6vyb - Comparative docking studies on curcumin with COVID-19 proteins 2020 R Suravajhala, A Parashar, B Malik, VA Nagaraj - 2020 - pdfs.semanticscholar.org were subjected to a 3D structure generation on CORINA [12] using their SMILE Preparation of proteins and grid parameters: The protein data bank ( PDB ) structures of different proteins were retrieved from RCSB membrane protein (6M17), polymerase (6M71), spike ( 6VYB )
134 5eks - Architecture and functional dynamics of the pentafunctional AROM complex 2020 HA Veraszt, M Logotheti, R Albrecht, A Leitner- Nature Chemical, 2020 - nature.com 2: The architecture and structural characteristics of the AROM complex. figure2. a, Definition of color scheme and order of domains in the CtAROM sequence, with gray numbers according to the succession of reactions in the pathway. b, CtAROM crystal structure with active sites ... The resulting representative PDB structures are 1NVA, 1XAL, 3QBD and 5EKS, for the DHQS
135 3uqa - AtFKBP53: a chimeric histone chaperone with functional nucleoplasmin and PPIase domains 2020 AK Singh, A Datta, C Jobichen, S Luan- Nucleic Acids, 2020 - academic.oup.com this PPIase with histone chaperoning activity, we have solved the crystal structures of its a pentameric nucleoplasmin-fold; making this the first report of a plant nucleoplasmin structure The crystal structure of AtFKBP53 FKBD (residues 360–477) was solved by molecular replacement method with the help of program MolRep (52) from CCP4 suite, using the coordinates of the A54E mutant of Burkholderia pseudomallei FKBP-FK506 complex structure as a search model (PDB ID: 3UQA), but without FK506.
136 4x54 - The mycolic acid reductase Rv2509 has distinct structural motifs and is essential for growth in slowgrowing mycobacteria 2020 A Javid, C Cooper, A Singh, S Schindler- Molecular, 2020 - Wiley Online Library structures of the four highest-scoring experimental SDRs (3ASU/3ASV, 1XG5, 4X54 and 4BMV based on the SDR from Sphingobium yanoikuyae (4BMV. pdb ; GenBank ID ACB78183.1 structure elements of Rv2509 aligned to its corynebacterial homologues, the core structure of
137 5u4s - Species-specific differences in the inhibition of 11-hydroxysteroid dehydrogenase 2 by itraconazole and posaconazole 2020 SG Inderbinen, M Zogg, M Kley, M Smieko- Toxicology and Applied, 2020 - Elsevier models were based on the template structure of 11-HSD1 (various PDB IDs), one model on the template structure of 3-oxoacyl-[acyl-carrier-protein] reductase ( PDB ID: 3u9l) and finally one on the template structure of a putative short chain dehydrogenase ( PDB ID: 5u4s )
138 6q05 - Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS 2020 JA Jaimes, NM Andre, JK Millet- arXiv preprint arXiv, 2020 - arxiv.org Protein Data Base: HCoV-HKU1 ( PDB # 5I08), MHV ( PDB # 3JCL), MERS-CoV ( PDB # 6Q05 ), SARS-CoV ( PDB # 5X58), FCoV-UU4 ( PDB # 6JX7), IBV-M41 ( PDB # 6CV0) and HCoV-NL63 ( PDB # 5SZS). Pairwise S structure . Additional
139 2lwk - Maicol Bissaro, Mattia Sturlese and Stefano Moro 2020 K Kuca, M Tutone, E Malinowska- In Silico Methods for Drug, 2020 - books.google.com against the PDB reference.(B) Superimposition between the experimental NMR complex ( PDB ID 2LWK , green-colored RMSD of RNA phosphate atoms belonging to the backbone, computed against the PDB reference E) Flexibility characterizing the RNA structure during DPQ
140 3hhe 3uw1 Biochemical and structural insights into an Ochrobactrum sp. CSL1 ribose-5-phosphate isomerase A and its roles in isomerization of rare sugars 2020 X Ju, X Xu, M Shen, X Mo, H Fan, L Liangzhi- Enzyme and Microbial, 2020 - Elsevier thermophilus (TtRpiA, 1UJ5), Burkholderia thailandensis (BtRpiA, 3UW1), Bartonella henselae (BhRpiA, 3HHE ) and E. coli (EcRpiA, 1O8B) with ligand-binding structures in PDB , the sequence Homology modeling is an option to investigate the structure -activity relationship of
141 5ucm - trans-Editing by aminoacyl-tRNA synthetase-like editing domains 2020 ABK Nagy, M Bakhtina- Biology of Aminoacyl, 2020 - books.google.com bound by an autonomous trans- editing factor, such as C. crescentus ProXp-ala ( PDB ID: 5VXB PheRS is also unique in its oligomeric structure it is a heterote- tramer domain ( bound in an editing active conformation will be needed to fully understand the structural basis for
142 4ix8 - Flavones reversibly inhibit Leishmania donovani tyrosine aminotransferase by binding to the catalytic pocket: An integrated in silico-in vitro approach 2020 S Sasidharan, P Saudagar- International Journal of Biological, 2020 - Elsevier TAT has also been characterized in Leishmania major [26], Leishmania donovani [10], and Leishmania infantum [8]. Furthermore, the crystal structure of the TAT from L. infantum has been solved ( PDB id: 4IX8 ) [27] and the structure contained PLP in the active site cavity bound
143 6dj8 - COMPARISON OF STRUCTURAL PROTEIN OF SILKWORM DENSOVIRUS BMDNV-1 WITH PROTEINS OF VIRUSES OF BACTERIA AND ARCHAEA TO STUDY THE POSSIBILITY OF FALSE POSITIVE ANSWERS IN THE ELISA - TESTING OF CATERPILLARS 2020 Antonovich ZA, Nazipova NN, ..., Scientific Journal of KubSAU , 2020 - ej.kubagro.ru PDB . . , SMTL ID : 6dj8 .1 ( Structure of DNA polymerase III subunit beta from Borrelia burgdorferi)
144 3vab - The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate 2020 VA Bielinski, JK Brunson, A Ghosh, MA Moosburner- bioRxiv, 2020 - biorxiv.org in the active site. The structure underscores features unique to the PtLYSA clan of DAPDC and provides structural insight into the determinants responsible for the substrate-promiscuity observed in PtLYSA. ... Akin to protomer 2 of PtLYSA, this segment is not included in the structures of DAPDC from Aquifex aeolicus (PDB 2P3E) and Brucella melitensis (PDB 3VAB).
145 4g7f 4iv5, 4fzi, 4lsm Synthesis of new N,S-acetal analogs derived from juglone with cytotoxic activity against Trypanossoma cruzi 2020 PAF Pacheco, T de Menezes Ribeiro- Journal of Bioenergetics, 2020 - Springer Naphthoquinones are considered important structures in medicinal chemistry due to their synthetic versatility and their v.1.0.1 program was used to build the molec- ular structure of ligands the best SI value among all molecules tested indicating that this structural feature might
146 5ucm - Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase 2020 J Zajac, H Anderson, L Adams, D Wangmo, S Suhail- The Protein, 2020 - Springer Identifying and understanding how these catalytic residues help enzymes achieve enormous rate enhancement has been the focus of many structural and biochemical studies over the past several decades Fig. 1 figure1. Structural model of E. coli ProRS
147 6q05 - Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus evolution 2020 J Yu, S Qiao, R Guo, X Wang- Nature communications, 2020 - nature.com structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus evolution. Download PDF. Article; Open Access; Published: 17 June 2020. Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus evolution
148 5i7w - Characterization of Cystathionine Synthase TtCbs1 and Cysteine Synthase TtCsa1 Involved in Cysteine Biosynthesis in Tetrahymena thermophila 2020 H Lv, J Xu, T Bo, W Wang- Journal of Eukaryotic Microbiology, 2020 - Wiley Online Library TtCsa1 has more than 30% sequence identities with B. abortus CS ( PDB ID: 5JIS) (Dharavath et al. 2017), B. suis CS ( PDB ID: 5I7W ), and L. major CS ( PDB ID: 4AIR) (Fyfe et al. 2012), and we modeled the overall structure of TtCsa1 with these crystal structures
149 5k85 - Selective inhibition of Zophobas morio (Coleoptera: Tenebrionidae) luciferaselike enzyme luminescence by diclofenac and potential suitability for lightoff 2020 MC Carvalho, A Tomazini, RA Prado- Luminescence, 2020 - Wiley Online Library tertiaricarbonis PDB file ID: 6HE0, Cryptococcus neoformans PDB file ID: 5K85 , Salmonella typhimurium PDB file ID: 5JRH) indicated that, among the five binding sites, that of CoA was structure and function prediction. Nat Protoc 2010; 5: 25-738. 49
150 6q05 - Distinct structural flexibility within SARS-CoV-2 spike protein reveals potential therapeutic targets 2020 SH Chen, MT Young, J Gounley, C Stanley, D Bhowmik- BioRxiv, 2020 - biorxiv.org of SARS-CoV-2 ( PDB 6VSB [3]), SARS-CoV-1 ( PDB 6CRZ [15]), MERS- CoV ( PDB 6Q05 [16]), and The trimeric state of the SARS-CoV-2 S protein consists of all three chains in PDB 6VSB Each structure was solvated in the center of a water box with a minimum distance of 15 A
151 6c9e 5vpr Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases 2020 JA Dunkle, MR Bruno, PA Frantom- Section D: Structural Biology, 2020 - scripts.iucr.org Q5ZXX6 6c9e , A L. pneumophila Lpg0604 Resting state Page 7 Six sequences/ structures belong to the IPR010970 SufS family by sequence homology, and inspection of these structures reveals that five possess the -hairpin structure and one, PDB entry 5vpr from
152 5dld - Structural characterization of a nonhydrolyzing UDP-GlcNAc 2-epimerase from Neisseria meningitidis serogroup A 2020 NK Hurlburt, J Guan, H Ong, H Yu, X Chen- Section F: Structural, 2020 - scripts.iucr.org The 9 9 loop in NmSacA also contains a 310-helix, which is not observed in the E. coli structure . The structures of other epimerases with ligands bound in the active site, including those from Burkholderia vietnam- iensis ( PDB entry 5dld ; 48.7% identity; Seattle Structural
153 4g7f - HUMANIDADES, CIENCIA, TECNOLOGA E INNOVACIN EN PUEBLA 2020 MG SOTO, C SUBCUTNEA - academiajournals.com Agarosa NTD Enfermedades Tropicales Desatendidas OMS Organizacin Mundial de la Salud ONU Organizacin de las Naciones Unidas OPS Organizacin Panamericana de la Salud PBS Buffer salino de fosfatos PBS-T Buffer salino de fosfatos-Tween 20 PDB Banco de
154 3s6l - Modelled structure of the cell envelope proteinase of Lactococcus lactis 2020 EB Hansen, P Marcatili- Frontiers in bioengineering and, 2020 - frontiersin.org The architecture of the L. lactis CEP shares features with a large number of serine proteases to use current state of the art structure prediction algorithms to establish a structural model of software (version 2.3.3)2 was used for visualization and editing of protein structure PDB files
155 4ed9 - Overexpression and Purification of the Protein BaiK for Structural Characterization by X-Ray Crystallography 2020 S Khuu - 2020 - broncoscholar.library.cpp.edu Initially , BaiK was overexpressed to produce large quantity of protein for use in structural and structure being very similar to histidine while also being added at a high concentration. 11 formation of more ordered crystal structures . The effective concentration of the protein
156 6c87 6dbb, 6nab, 6byq Exploring Unconventional Approaches to Molecular Replacement in X-ray Crystallography with SIMBAD 2020 AJ Simpkin - 2020 - search.proquest.com to finding search models for MR is to use the sequence of the target structure to identify a approach is based on the assumption that sequence similarity is a useful guide to structural similarity final step is a brute-force search of a non-redundant derivative of the PDB provided by
157 5VOG - Structural analysis of (p) ppGpp reveals its versatile binding pattern for diverse types of target proteins 2020 GS Kushwaha, A Patra, NS Bhavesh- Frontiers in microbiology, 2020 - ncbi.nlm.nih.gov Although, glycosidic bond and ribose sugar in the nucleotide structure exhibit conformational flexibility and classical molecular dynamics simulation on nucleotides is S.No, Macromolecule Name, Resolution (), PDB ID 14, Putative phosphoribosyltransferase, 1.50, 5VOG
158 6vxx - Developing a fully glycosylated full-length SARS-CoV-2 spike protein model in a viral membrane 2020 H Woo, SJ Park, YK Choi, T Park- The Journal of, 2020 - ACS Publications This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-l...
159 4lsm 4k9d, 6ok4 Estudos estruturais das enzimas urocanato hidratase de Trypanosoma cruzi, gliceraldedo-3-fosfato desidrogenase de Schistosoma mansoni e glicose-6-fosfato-1 2020 S Boreiko - 2020 - tede2.uepg.br the conformation of monomers A and C, which were explored to understand structural changes in 1-Epimerase, also part of the glycolytic pathway, had its structure modeled by e Homo sapiens 2 (cdigo PDB 3H9E), Trypanosoma cruzi (cdigo PDB 4LSM ), Arabidopsis thaliana
160 6ws6 - Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2 2020 JB Case, PW Rothlauf, RE Chen, Z Liu, H Zhao- Cell host &, 2020 - Elsevier Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput-imaging-based neutralization assay at biosafety level 2 ... VIR antibody set Pinto et al., 2020 S309 PDB: 6WS6
161 3ixc - Crystal structure and active site engineering of a halophilic -carbonic anhydrase 2020 M Vogler, R Karan, D Renn, A Vancea- Frontiers in, 2020 - frontiersin.org (C) The surface potential of CA_D compared to mesophilic -CA homologs (Escherichia coli, 3tio; Salmonella enterica, 3r3r; Anaplasma phagocytophilum, 3ixc ; Bacillus cereus, 1xhd (A) CA_D (crystal structure ), (B) Cam (crystal structure ) from M. thermophila ( PDB ID: 1qrg
162 3gwc - Mechanism of naphthoquinone selectivity of thymidylate synthase ThyX 2020 H Myllykallio, HF Becker, A Aleksandrov- Biophysical Journal, 2020 - Elsevier to be very small, less than 0.1 kcal mol 1 . To model C8-C1 in complex with ThyX from Mtb, the C8-C1 ligand from the crystal structure from PBCV-1 was retained after superimposing the crystal structures from ThyX and PBCV-1( PDB : 4FZB, 3GWC ) using the
163 6q04 - Controlling the SARS-CoV-2 spike glycoprotein conformation 2020 R Henderson, RJ Edwards, K Mansouri- Nature structural &, 2020 - nature.com d, The SARS-2 (left, PDB 6VXX) and MERS (right, PDB 6Q04 ) structures , each with a single protomer depicted in cartoon of the gj angles and dihedrals overlaid on an alignment between a SARS-2 down (cartoon structure with black centroids and lines; PDB 6VXX) and
164 6wpt - A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction 2020 M Ejemel, Q Li, S Hou, ZA Schiller, JA Tree- Nature, 2020 - nature.com COVID-19 caused by SARS-CoV-2 has become a global pandemic requiring the development of interventions for the prevention or treatment to curtail mortality and morbidity. No vaccine to boost mucosal immunity, or as a therapeutic, has yet been developed to SARS-CoV-2. ... However, this predicted epitope of MAb362 is different from the other recently reported MAb complexes to the SARS-CoV-2-RBD (Fig. 3c and Supplementary Fig. 5), including: CR302217 (PDB: 6W41); S30916 (PDB: 6WPT); REGN10933 and REGN1098725;
165 3r8c 4die, 3r20 The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor 2020 R Mega, N Nakagawa, S Kuramitsu, R Masui- PloS one, 2020 - journals.plos.org open form, CMP-bound closed form, ADP-CDP-Gd 3+ -, and CDP-bound forms at resolutions of 1.7, 2.2, 1.5, 1.6, and 1.7 , respectively (Table 1, Fig 1). Structural differences between (B) Superimposition of the overall structure of ligand-free form (gray; PDB code 3W90 ... and ligand-free form of CMPK from M. abscessus (dark gray; 3R8C). These structures were structurally aligned ... The ligand-free form of M. smegmatis CMPK (PDB code 3R20) is almost the same structure as M. abscessus CMPK.
166 5bt8 - Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea 2020 M Rojas-Pirela, D Andrade-Alvirez- Open, 2020 - royalsocietypublishing.org bacteria, PGK, monomer, open, , 6I06, [39]. Acinetobacter baumannii, bacteria, PGK, monomer, , , 5BT8 , Fairman et al. (NA) Figure 3. Three-dimensional structure of phosphoglycerate kinase. (a) Ribbon representation of the overall structure of pig muscle PGK ( PDB : 1HDI)
167 6vyb - Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination 2020 SA Ahmed, DA Abdelrheem, HR Abd El-Mageed- Structural Chemistry, 2020 - Springer Protein preparation. The 3D crystal structure of the SARS-CoV-2 main protease Mpro ( PDB ID: 6LU7) and the cryo-electron microscopic structure of the SARS-CoV-2 spike protein Sp ( PDB ID: 6VYB ) were taken from the PDB (Protein Data Bank) site
168 6mb1 - Profiling of myristoylation in Toxoplasma gondii reveals an N-myristoylated protein important for host cell penetration 2020 M Broncel, C Dominicus, L Vigetti, SD Nofal, EJ Bartlett- Elife, 2020 - elifesciences.org structure with bound IMP-1002 ( PDB : 6MB1 , [Schlott et al., 2019]) revealed high sequence identity (57%) and showed that all residues directly involved in compound binding are conserved within the TgNMT active site and therefore predicted to adopt an identical structural
169 6nb8 - Drug Targets for Corona Virus (COVID-19): A Systematic Review 2020 K Jayakumar - 2020 - saudijournals.com to neutralize it, and their structures are also available ( PDB IDs: 6NB6, 6NB7, and 6NB8 .The monoclonal antibody, m396, has a competitive role for RBD binding ( PDB ID: 2DD8 However, the structure is highly variable among different members of the CoV family
170 4odj - Nucleoside-modified AdoMet analogues for differential methyltransferase targeting 2020 NV Cornelissen, F Michailidou, F Muttach- Chemical, 2020 - pubs.rsc.org 39 In addition, we tested the putative wildtype MAT from Cryptosporidium hominis (ChMAT) that had been crystallized by the Seattle Structural Genomics Center for Infectious Disease (SSGCID) but was otherwise ChMAT ( PDB : 4ODJ ) and hMAT2a ( PDB : 5A1G) have 59
171 3gbz - How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase family 2020 Z Shamsi, D Shukla- Molecular Systems Design & Engineering, 2020 - pubs.rsc.org PDB ID: 5OSM, 6Q3F, 6Q4A, 6Q4B, 6Q4C, 6Q4D, 6Q4K), G/CDK ( PDB ID: 3GBZ ), and pfpk5 on the GA341 score and have comparable DOPE scores with the CDK2 native structure as shown Template's PDB ID, DOPE score for CMGI, DOPE score for native CDK2, GA341 score
172 3rd5 - In silico structural analysis and ligand-binding predictions of a few developmental stage specific-proteins during in vitro morphogenesis in Vanilla 2020 M Sultana, G Gangopadhyay- Vegetos, 2020 - Springer The crystal structure of anoxidoreductase protein (a putative uncharacterized protein from Mycobacterium paratuberculosis, PDB ID- 3RD5 ) was used as a template to predict the three dimensional model (Fig. 5e) of it. The predicted docking model (Fig
173 5vm8 - Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites 2020 AP Perlinska, A Stasiulewicz- PLOS Computational, 2020 - journals.plos.org depicted with rainbow coloring (TrmD, PDB ID: 4yvg), (B) unknotted methyltransferase (Trm5, PDB ID: 2zzm On the top of this it was shown that the structure of the knotted core Different conformations of the ligand imply differences in both structural and chemical characteristics of
174 5j3b - Structure and Function of an Elongation Factor P Subfamily in Actinobacteria 2020 B Pinheiro, CM Scheidler, P Kielkowski, M Schmid- Cell Reports, 2020 - Elsevier In order to gain insights into the structural configuration of this Actinobacteria EF-P, we X-ray crystal structure to 2.2- resolution (for data processing and structure refinement statistics its overall folding topology with the previously reported bacterial EF-P structures and consists of
175 3tsm - Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa-decarboxylation is not essential for indole formation 2020 A Sderholm, MS Newton, WM Patrick- Journal of Biological, 2020 - ASBMB catalytic residues taking part in the dehydration step are harder to speculate on due to the substantial structural rearrangements taking However, a different open conformation of helix 0 is observed in the structure of IGPS from Brucella melitensis ( PDB 3TSM , unpublished
176 5b8i - Two SnRK2-interacting calcium sensor isoforms negatively regulate SnRK2 activity by different mechanisms 2020 K Tarnowski, M Klimecka, A Ciesielski, G Goch- Plant, 2020 - Am Soc Plant Biol Skip to main content
177 6nb6 - Recognition of Potential COVID-19 Drug Treatments through the Study of Existing ProteinDrug and ProteinProtein Structures: An Analysis of Kinetically Active 2020 O Perii- Biomolecules, 2020 - mdpi.com their binding free energies to the COVID-19 structural and non- structural protein sites The structure alignment, hydrophobicity calculation, visualization and analyses were performed with the programs Chimera each protein chain that forms a protein complex (given as a PDB file
178 4hjh - Genomic Analysis of Natural Rough Brucella melitensis Rev. 1 Vaccine Strains: Identification and Characterization of Mutations in Key Genes Associated with 2020 D Kornspan, R Lubkovskaia, S Mathur- International journal of, 2020 - mdpi.com through all homologs (Figure 2A). To evaluate the possible effect of the detected mutation on protein functionality, we conducted a structural analysis of the amino acid sequence of GST based on the solved 3D structure of this protein from Sinorhizobium meliloti ( PDB ID 4MDC) ... we conducted a structural analysis of the amino acid sequence of phosphomannomutase based on the solved 3D structure of its paralog phosphoglucomutase (PDB ID 4HJH,
179 3o0h - Structure of flavoprotein RclA from food-borne pathogens, and its molecular mechanism contributing to hypochlorous acid resistance 2020 - 2020 - s-space.snu.ac.kr representation is labeled with residue numbers of three proteins (first RclA, second 3O0H , third 4M52). Page 36. 26 3.4 I searched for the closest protein to RclA in terms of structure using the DALI server (30). Mercuric reductase (MerA) ( PDB code: 4K7Z), a group II FDR
180 6nb6 6nb7 Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2 2020 A Basu, A Sarkar, U Maulik- Scientific reports, 2020 - nature.com Every coronavirus comprises four structural proteins namely spike, envelope, nucleocapsid and membrane proteins Similarly, PDB ID 6M17 shows the presence of sodium-dependent neutral amino acid transporter B(O)AT1 in its structure
181 4f82 4f4a Investigating Imatinib-Resistant Mutations in Abl Kinase 2020 A Lyczek - 2020 - search.proquest.com 10 *(52& Illustration of important structural features of imatini<
182 6q04 - Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate 2020 S Bangaru, G Ozorowski, HL Turner- , 2020 - science.sciencemag.org Report. Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate 1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
183 3u0g - Counterbalance of Stability and Activity Observed for Thermostable Transaminase from Thermobaculum terrenum in the Presence of Organic Solvents 2020 EY Bezsudnova, AY Nikolaeva, SY Kleymenov- Catalysts, 2020 - mdpi.com the hydration shell and the interface of the enzyme molecules, thus defining the balance between the structural integrity and Somewhat counterintuitively, crystallographic studies of solvent-resistant enzymes did not reveal significant changes in structures obtained from crystals
184 4dz4 - The neighboring subunit is engaged to stabilize the substrate in the active site of plant arginases 2020 B Sekula- Frontiers in plant science, 2020 - frontiersin.org It is worth noting that the structure of agmatinase from Deinococcus radiodurans ( PDB ID: 1WOG) (Ahn et al., 2004) is ID: 3LHL), agmatinase from Thermoplasma volcanium (TvAGM, PDB ID: 3PZL), and agmatinase from Burkholderia thailandensis (BtAGM, PDB ID: 4DZ4 )
185 3tcq - Common substructures and sequence characteristics of sandwich-like proteins from 42 different folds 2020 A Kister- BioRxiv, 2020 - biorxiv.org structural classification in PDBSum database30 does not support sandwich-like architecture was examined. For secondary structure analysis, the information about localization of strands in sequences was taken from PDB .31 For supersecondary structure (SSS) of the domains
186 4iv5 - Theory, Design and Characterization of Protein Symmetry Combination Materials 2020 J Laniado - 2020 - search.proquest.com The symmetry group of a structure can be used to understand how many structurally distinct contact types are required to hold all the Current Opinion in Structural Biology 2016, 39:134143 built into a protein building block in order for it to assemble into the desired architecture
187 2kn9 - A new twist of rubredoxin function in M. tuberculosis 2020 T Sushko, A Kavaleuski, I Grabovec, A Kavaleuskaya- bioRxiv, 2020 - biorxiv.org 21]. Previously, a zinc-substituted RubB structure was solved by NMR ( PDB ID: 2KN9 ). Pairwise . In the NMR model, residues at C and N termini show backbone variability, while the rest of the structure remain almost unperturbed
188 6amz - Identification of potential therapeutic targets in Neisseria gonorrhoeae by an in-silico approach 2020 P Tanwer, SRR Kolora, A Babbar, D Saluja- Journal of Theoretical, 2020 - Elsevier The obtained protein. pdb file was overlapped with the homologous protein whose crystal structure ( 6AMZ from Acinetobacter baumannii) was obtained from RCSB database (Berman et al., 2000). Both protein structures were overlapped using Pymol (Alexander et al., 2011) to
189 3s6d - Leptospira interrogans triosephosphate isomerase: exploring the structural determinants of stability, high reaction rate and specificity. 2020 V Pareek, V Dhayabarn, H Balaram, PR Krishnaswamy- bioRxiv, 2020 - biorxiv.org Contrary to our observation for the LiTIM structure , the backbone -CO of Trp11 has previously been observed in other TIMs (eg Page 15. 15 rare example of Glu at position 94 (LiTIM numbering) is in Coccidiodes immitis ( PDB ID: 3S6D ; Figures S2 and S5B)
190 4g7f - In silico repositioning of etidronate as a potential inhibitor of the Trypanosoma cruzi enolase 2020 EA Valera-Vera, M Say, C Reigada- Journal of Molecular, 2020 - Elsevier Preparation of the PDBQT files (Protein Data Bank, partial charge (Q), and atom type (T)) was performed using AutoDock Tools v1.5.6 [29]. A search in the Protein Data Bank ( PDB ) [30] was carried to find the crystal structure of TcENO ( PDB ID: 4G7F , Resolution: 2.4 , R
191 6ar7 - Learning Super-Resolution Electron Density Map of Proteins using 3D U-Net 2020 B Mullick, Y Wang, P Yadav, AB Farimani - mlsb.io The mesh grid displays the electron density surface for the structure and the underlying line diagram represents the protein structure from the PDB file. (a) The electron density map of PDB ID: 6AR7 (Green), with resolution of 2.10
192 4q04 - Structural and functional diversity of Entamoeba histolytica calcium-binding proteins 2020 S Kumar, S Mishra, S Gourinath- Biophysical Reviews, 2020 - Springer 78% identical). Here, along with the reported structures of amoebic CaBP1, CaBP2, CaBP3, and CaBP5, we have complied the structural information of an unpublished structure of EhCaBP19 ( PDB deposited) as well. In this
193 6tys - Structural insight into paramyxovirus and pneumovirus entry inhibition 2020 M Aggarwal, RK Plemper- Viruses, 2020 - mdpi.com 19,20,21] have furthermore created a novel opportunity for structure -informed mechanistic Structural information is very limited compared to that available for the paramyxovirus attachment Consequently, crystal structures of prefusion PIV5 and NiV F ectodomains could only be
194 4jgb 4jga TAK1: a potent tumour necrosis factor inhibitor for the treatment of inflammatory diseases 2020 J Totzke, SA Scarneo, KW Yang- Open, 2020 - royalsocietypublishing.org A general core structure for type II binders has been developed, consisting of a hydrophobic moiety Structural disorder of this region is often cited as a reason for the missing residues of Ligand 10 (purple, PDB 4JGA), 11 (orange, PDB 4JGB ) and 12 (dark green, PDB 4JGD) are
195 4dgq - Structural and Biophysical Characterization of human NDRG3, a key component of lactate-induced hypoxia responses 2020 - 2020 - s-space.snu.ac.kr 85 Figure 49 Structural comparison of C rmsd values at 5 mM and 87 Figure 51 Molecular dynamic simulation on NDRG3 C30S structure for 100 picoseconds PCR Polymerase chain reaction PDB Protein data bank PEG Polyethylene glycol
196 4g5d - Leishmania braziliensis prostaglandin F2 synthase impacts host infection 2020 EVC Alves-Ferreira, TR Ferreira, P Walrad, PM Kaye- Parasites & vectors, 2020 - Springer 1b) and the 3D structure (Fig c 3D sequence alignments of protein sequences of LmjPGF2S (PBD ID 4G5D , in grey) and human ortholog 51.4% similarity and 34.3% identity, modelling using the Research Collaboratory for Structural Bioinformatics (RCSB) PDB suggests that
197 4twr - Molecular evolution and functional divergence of UDP-hexose 4-epimerases 2020 S Fushinobu- Current Opinion in Chemical Biology, 2020 - Elsevier Figure 3. Structural basis for the substrate specificity of group 1b and group 2b enzymes The rotated conformation structure was obtained using the S124A/Y149F double mutant ... Substrate-free structures of GalEs from Bacillus anthracis (BAS5114, PDB: 2C20) and Brucella abortus (PDB: 4TWR) are also available in the database
198 6q06 - Convergent structural features of respiratory syncytial virus neutralizing antibodies and plasticity of the site V epitope on prefusion F 2020 W Harshbarger, S Tian, N Wahome, A Balsaraf- PLoS, 2020 - journals.plos.org ]To fully elucidate the RSB1 paratope and the targeted PreF epitope architecture and better understand the competition with multiple antigenic sites, we determined the crystal structure of the ... Surface potential around PreF residue Asn200 from the structure of RSV B PreF PDB 6Q06 (left), with the RSB1 interacting residue Arg53(LCDR2) is shown again for comparison
199 3lr0 - The role of hydrophobic interactions in folding of -sheets 2020 J Li, X Ma, H Zhang, C Hou, L Shi, S Guo- arXiv preprint arXiv, 2020 - arxiv.org Nature Structural Biology 10, 980, doi:10.1038/nsb1203-980 (2003). 19 Berman, H., Henrick, K., Nakamura, H. & Markley, JL The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data Structure relaxation via long trajectories made stable
200 2mj3 - Understanding and modulating electron transfer through ferredoxins 2020 I Campbell - 2020 - scholarship.rice.edu 3.6. Cyanophage Fd structural characterization ..... 79 This bioinformatic study highlights understudied PECs whose structure , stability, and partner specificity should be further characterized... 1UWM, 1PDX, 1M2D, 1I7H, 3AH7, 2MJD, 2MJ3, 2Y5C, 5FFI, 3P1M, 1E0Z, 1DOI
201 5ucm - Human trans-editing enzyme displays tRNA acceptor-stem specificity and relaxed amino acid selectivity 2020 O Vargas-Rodriguez, M Bakhtina, D McGowan- Journal of Biological, 2020 - Elsevier Corrections to the resulting alignment were made based on the structural alignment of Cc ProXp-ala (Protein Data Bank entry 5VXB) and Pa ProRS (Protein Data Bank entry 5UCM).
202 5j3b - How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology 2020 W Casey, S Massey, B Mishra - 2020 - researchsquare.com Here we will further illustrate and discuss the sur- prisingly diverse dynamics expressed for a variety of population structures The process architecture is simple, but worth noting that each type in the population structure forms a component in the evolution processes ... factor (1EH1), Acinetobacter baumannii elongation factor P (5J3B), T.thermophilus
203 6pqh - Development of Novel Antibacterial Agents through the Design and Synthesis of Aminoacyl tRNA Synthetase (AaRS) Inhibitors 2020 H Asiri, C Simons, E Mantzourani - 2020 - orca.cf.ac.uk 33 Figure 16: Chemical structures of LysRS and AspRS inhibitors. 34 Figure 17: Chemical structures of AsnRS and AlaRS inhibitors. 34 Figure 21: 3D structure of Thermus thermophilus AsnRS ( pdb : 5ZG8) with two-8 amino acid residues gaps (161-168 and 209-216) identified. Table 7. Elizabethkingia anopheles 6PQH
204 6nb7 - Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital 2020 H Lim, A Baek, J Kim, MS Kim, J Liu, KY Nam- Scientific reports, 2020 - nature.com the hot spot region, we also performed the same calculation with RBD-SARS-CoV-1/antibody complexes (five experimental structural data All experimental structures calculated in this work are summarized in Table 1. All missing side chains were filled using Prime implemented
205 3r9r - APPLICATIONS OF SPERMINE AND DERIVATIVES THEREOF 2020 W Pan, W Zhu- US Patent App. 16/889,500, 2020 - freepatentsonline.com pneumonia (4FGR, 4FE2), Mycobacterium abscessus ATCC 19977/DSM 44196 ( 3R9R ), Thermotoga maritime On the basis of the above results, the crystal structure conformations in synthetases of Saccharormyces cerevisiae ( PDB : 2CNQ) and Escherichia coli ( PDB : 2GQS) are
206 4xwi - A study of Rose Bengal against a 2-keto-3-deoxy-d-manno-octulosonate cytidylyltransferase as an antibiotic candidate 2020 S Kim, S Jo, MS Kim, DH Shin- Journal of enzyme inhibition and, 2020 - Taylor & Francis The atomic coordinates of the crystal structure of PaKdsB ( PDB ID: 4XWI ) were saved from the Protein Data Bank and prepared by The crystal structure of PaKdsB deposited in the Protein Data Bank was retrieved and docked with Rose Bengal to predict its binding mode
207 4q14 - HISTIDINE PROTONATION AS A POSSIBLE MECHANISM FOR HUMAN TRANSTHYRETIN AMYLOIDOSIS: MODELLED AGAINST WALLABY 2020 DG D'SOUZA - 2020 - researchrepository.rmit.edu.au 0.97 indicated a highly conserved overall structure between the solved structure of wallaby TTR and a known crystal structure of human TTR ( PDB : 3U2I). The structural homology was strong with an almost perfect overlap of their peptide backbones, secondary, tertiary and ... Table 3.3 Predicted model of human TTR compared to other structurally similar proteins 7 4Q14 Brucella 0.806 1.62 0.283 0.890
208 4iuj - Toward a PA-Inhibitor Complex Crystal System: Influenza Polymerase Acidic Protein Fusion Constructs and Protein Expression 2020 R Kramb - 2020 - ecommons.udayton.edu Figure 5 b (right) apo-PA crystal packing. PA ( PDB ID: 4IUJ ) is rendered as a surface, and a loop interest, our approach is to create different protein fusions of PA that will alter the crystal packing structure of PA, which could allow the visualization of the apo protein through
209 4eqy - Structure-Based Virtual Screening of Pseudomonas aeruginosa LpxA Inhibitors Using Pharmacophore-Based Approach 2020 BV Bhaskar, TMC Babu, A Rammohan, GY Zheng- Biomolecules, 2020 - mdpi.com 1J2Z) [22], Leptospira interrogans ( PDB ID: 3HSQ) [23] and Burkholderia thailandensis ( PDB ID: 4EQY ) [24] were In this study, the PaLpxA structure was superimposed on LpxA orthologs from different bacterial Organism PDB ID Monomer A Monomer B RMSD () Pocket Size (
210 6q05 - A Review of Current Literature on sudden Upsurge of COVID-19 2020 R Sharma- Annals of Tropical Medicine and Public, 2020 - journal.atmph-specialissues.org 6Q05 MERSCoV S structure in complex with SialylLewis Available from: http://www.rcsb.org/ pdb /results/results.do?tabtoshow=Unreleased and qrid=7E90BED0 coronavirus papain-like novel protease inhibitors: Design, synthesis, protein-ligand X-ray structure and biological
211 6nb6 6nb7 Computational approach for the design of potential spike protein binding natural compounds in SARS-CoV2 2020 A Basu, A Sarkar, U Maulik - 2020 - researchsquare.com 2dd8:S, 2ghw:A, 1q4z:A, 1t7g:A, 1xjp:A, 5xlr:A, 5x58:A, 6nb6 :A, 6nb7 ASN 448 are also conserved in ve SARS CoV-2 spike protein PDB structures and changed in SARS-CoV 21. Guex, N., Peitsch, MC, Schwede, T. Automated comparative protein structure modeling with SWISS
212 3f0d - Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins 2020 M Macchiagodena, M Pagliai, C Andreini, A Rosato- ACS, 2020 - ACS Publications Journal Logo. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. Marina Macchiagodena Marina Macchiagodena. Dipartimento di
213 6bla - Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step 2020 X Ye, H Su, D Wrapp, DC Freed, F Li, Z Yuan- PLoS, 2020 - journals.plos.org A 1.8 crystal structure of 325 Fab in complex with the peptide epitope revealed the molecular determinants of 325 binding to gB A molecular replacement solution was found in PHASER [67] by using a search ensemble generated from PDB IDs: 6BLA and 6DDM.
214 4zju - Ternary complex formation of AFN1252 with Acinetobacter baumannii FabI and NADH: Crystallographic and biochemical studies 2020 NK Rao, V Nataraj, M Ravi- Chemical Biology &, 2020 - Wiley Online Library 6AHE) with the NAD bound AbFabI ( PDB :4JZU) (243 C atoms; PDB ; 4ZJU ),showed an rms Structural superposition revealed no major conformational changes except in The crystal structure of AbFabI in the ternary complex is similar to the reported structures of EcFabI
215 3gwc - dUMP/F-dUMP Binding to Thymidylate Synthase: Human Versus Mycobacterium tuberculosis 2020 K Gaurav, T Adhikary, P Satpati- ACS omega, 2020 - ACS Publications Thymidylate synthase is an enzyme that catalyzes deoxythymidine monophosphate (dTMP) synthesis from substrate deoxyuridine monophosphate (dUMP). Thymidylate synthase of Mycobacterium tuberculosis (... (a) X-ray structure of MtbThyX (homotetramer; monomeric units are in yellow, cyan, green and purple, PDB 3GWC(16)). Each ligand-binding site (out of four) is at the intersection of three monomeric units.
216 2khp - Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead 2020 RB Khattri, DL Morris, SM Bilinovich, E Manandhar- Molecules, 2020 - mdpi.com between the two domains, the presence of multiple paralogs in one or both species, and a lack of conserved genomic architecture between the Structural comparison of hGRX1 to E. coli GRX and BrmGRX indicated similarities in the overall fold and structure ... NMR backbone resonance assignments for BrmGRX (2KHP) and hGRX1 (1JHB) were obtained from the BMRB
217 6tz8 - Current Challenges and Opportunities in Designing ProteinProtein Interaction Targeted Drugs 2020 WH Shin, K Kumazawa, K Imai- and Applications in, 2020 - ncbi.nlm.nih.gov Phase Reached*, Modality*, Drug PDB ID**, Drug-Protein PDB ID*, Target PPI PDB ID binding protein 1A inhibitor, Inhibitor, Approved (1994), Small molecule, FK5, 1BKF, 6TZ8 (FKBP12/CNA 2.8 resolution by cryo-electron microscopy (cryo-EM).65 The cryo-EM structure revealed ... 6TZ8 (FKBP12/CNA/CNB) (C. neoformans)
218 6bfu 6q06, 6nb7, 6nb4, 6q07, 6q05, 6nb3, 6q04 Systematic modeling of SARS-CoV-2 protein structures 2020 SI O'Donoghue, A Schafferhans, N Sikta, C Stolte- bioRxiv, 2020 - biorxiv.org CoV, 82% identity, E = 10-24) with a fold not seen in any other PDB structure (CATH 3.40 from SARS-CoV-2, 98% identity, E = 10-44), all with beta barrel architecture (CATH 2.40 6acg from SARS-CoV, 77% identity, E = 10-321), of which one structure also showed
219 3mx6 - P1 Residue-Oriented Virtual Screening for Potent and Selective Phosphinic (Dehydro) Dipeptide Inhibitors of Metallo-Aminopeptidases 2020 M Talma, A Mucha- Biomolecules, 2020 - mdpi.com 20 to keep the size similar to the grid from the first step (36 for PDB : 2EK8 In general, the structure proposed here surpasses known inhibitors As the overall architecture of the S1 binding sites of porcine, bacterial, and protozoal APNs is rather conserved, the advantageous ... Table 1. Cont. Rickettsia prowazekii 3MX6 [41]
220 4hvt - Characterization and rational design for substrate specificity of a prolyl endopeptidase from Stenotrophomonas maltophilia 2020 J Yu, J Wu, D Xie, L Du, YJ Tang, J Xie- Enzyme and Microbial, 2020 - Elsevier from Rickettsia typhi ( PDB ID: 4 HV T, https://www.rcsb.org/ structure / 4HVT ) as template The structure of SmPEP was built by the Swiss Model server and crystal structure ( PDB ID: 4 On the basis of the simulated structure , Arg263 cannot form the original ring stacking with Phe479
221 3p96 - Identification and Repurposing of Trisubstituted Harmine Derivatives as Novel Inhibitors of Mycobacterium tuberculosis Phosphoserine Phosphatase 2020 E Pierson, M Haufroid, TP Gosain, P Chopra, R Singh- Molecules, 2020 - mdpi.com SerB2 model generated by homology modeling based on the crystal structure of Mycobacterium avium SerB (Protein Data Bank ( PDB ) entry 3P96 ) is in The docked structure of the best inhibitor, compound 124, is shown in Figure 4. Analysis of those structures shows that
222 5unb - Janus kinase inhibition for autoinflammation in patients with DNASE2 deficiency 2020 Y Hong, M Capitani, C Murphy, S Pandey- Journal of Allergy and, 2020 - Elsevier Structural modelling Structural models and figures were prepared using the ICM software package (Molsoft). A homology model for human DNase II was prepared using the existing structure from Burkholderia thailandensis ( PDB 5unb ) as the model template
223 4wi1 - Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches 2020 DW Nyamai, Tastan Bishop- International Journal of Molecular, 2020 - mdpi.com (B) 2D representation of (a) SANC184; (b) SANC257; (c) SANC264; (d) SANC456; (e) SANC622 (f) TCMDC-124506 ( PDB ID: 4WI1 ); (g) glyburide ( PDB ID: 5IFU SANC236 ligand was unstable during the 20 ns simulation with structure flips at 10, 30, 95, 160, and 180 ns of the
224 6wpt - Fruitful neutralizing antibody pipeline brings hope to defeat SARS-Cov-2 2020 A Renn, Y Fu, X Hu, MD Hall, A Simeonov- Trends in pharmacological, 2020 - Elsevier and a receptor-binding subdomain also referred to as receptor binding motif (RBM, residues 438505) which loops out of the core domain structure to directly The structures used for superimposition of S309 and CR3022 are with RBD of SARS-CoV-2 ( PDB 6WPT [41] and
225 3h81 - Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase 2020 J Hwang, CS Jeong, CW Lee, SC Shin, HW Kim- Journal of, 2020 - Springer (D) The electrostatic surface potential of the trimeric HyECH structure also shows that the periphery of the putative ligand-binding site has a positive charge MtECH, ECH from M. tuberculosis ( PDB code 3H81 ). Page 7. Crystal structures of BoECI and HyECH 7
226 6od8 - Leishmanial aspartyl-tRNA synthetase: Biochemical, biophysical and structural insights 2020 GC Panigrahi, R Qureshi, P Jakkula, KA Kumar- International Journal of, 2020 - Elsevier Furthermore, CD and intrinsic tryptophan fluorescence measurements showed the changes in structural conformation at varying pH, denaturants and ligands. The modelled LdaspRS structure presented all the specific characteristics of class II aaRSs, ... The three-dimensional structure of LdaspRS was predicted by homology modelling using Modeller 9.16 [22] with Leishmania major Friedlin aspartyl tRNA synthetase (PDB ID: 6OD8) as a template.
227 3tjr - On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment 2020 LM Longo, J Jablonska, P Vyas, R Kolodny, N Ben-Tal- bioRxiv, 2020 - biorxiv.org between Rossmanns and P-loops, ideally with respect to not only structure but also sequence 2003.1.1.417; PDB : 1k2w) and short chain dehydrogenase (F-Group 2003.1.1.332; PDB : 3tjr ) showing the highest overlap (Figure 4)
228 3jvi - In Silico Laboratory: Tools for Similarity-Based Drug Discovery 2020 S Lenik, J Konc- Targeting Enzymes for Pharmaceutical Development, 2020 - Springer The output file 1phrA_3jviA.0.rota. pdb contains 3jvi's coordinates superimposed onto 1phr according to Information window contains the name, PDB , and UniProt number of the clicked amino acid Sequence variants that could not be mapped to the protein structure are listed
229 5i1f - GTP Preference of d-Glycero--d-manno-Heptose-1-Phosphate Guanylyltransferase from Yersinia pseudotuberculosis 2020 S Kim, MS Kim, S Jo, DH Shin- International Journal of Molecular, 2020 - mdpi.com 2). In the case of GalU from Burkholderia vietnamiensis (BvGalU, PDB ID: 5I1F ), there are two In contrast, some of AMPPN bound structures can be searched in the PDB ( PDB ID: 5KQ8 an induced-fit conformational change when they interact with GMPPN in the crystal structure
230 4wny - A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis 2020 A O'Connor, R Berisio, M Lucey, K Schaffer, S McClean- bioRxiv, 2020 - biorxiv.org abilities. 253 To identify structural determinants responsible for the different behaviours of USP76 and 254 USP92, in particular their different abilities to bind to epithelial cells, we used homology 255 modelling and analysed resulting structures the best template was the BupsA stress protein from Burkholderia pseudomallei (PDB code 563 4wny, seqid 69.2%).
231 5k85 5ifi ProtCID: A data resource for structural information on protein interactions 2020 Q Xu, RL Dunbrack- Nature communications, 2020 - nature.com While the structure of full-length activated PAH has not been determined, a recent structure of the ACT domain of J9VFT1_CRYNH, E5XP76_9ACTN) and two common entries ( PDB : 5IFI [https://doi.org/10.2210/pdb5IFI/ pdb ] and 5K85 [https://doi.org/10.2210/pdb5K85/ pdb ])
232 6q04 - Human coronavirus spike protein-host receptor recognition 2020 L Guruprasad- Progress in biophysics and molecular biology, 2020 - Elsevier cause infection. In this review, we discuss structural features of HCoV spike proteins and recognition of host proteins and carbohydrate receptors. Keywords. Human coronavirus. SARS-CoV. SARS-CoV-2. MERS-CoV. HCoV-HKU1.
233 5umh - Estimating Change in Foldability Due to Multipoint Deletions in Protein Structures 2020 A Banerjee, A Kumar, KK Ghosh- Journal of Chemical, 2020 - ACS Publications Figure S6: Root mean-square fluctuation of each residue of the protein in its original conformation (in magenta) and of the protein subject to MPD in residue stretches in the nonloop region (in sea green) for PDB IDs: 4XGQ chain A, 5UMH chain A, 4A5M chain A, 3GUD chain A, and...
234 6q04 6VXX N-terminal domain (NTD) of SARS-CoV-2 spike-protein structurally resembles MERS-CoV NTD sialoside-binding pocket 2020 M Awasthi, S Gulati, DP Sarkar, S Tiwari, S Kateriya - 2020 - researchsquare.com W program [14]. Structure preparation The cryo-EM structures of SARS-CoV-2 ( PDB ID: 6VXX) [8] and MERS-CoV ( PDB ID: 6Q04 ) [10] spike spike glycoprotein (YP_009724390. 1) was strongly biased on the crystal structure of SARS-CoV-2, while
235 4f4f 3v7n Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major 2020 RJ Meshram, KT Bagul, SU Aouti, AM Shirsath- Molecular Diversity, 2020 - Springer conformational changes. Moreover, we address some important structural and dynamic interactions in the PLP binding region of TS that are in good agreement with previously speculated crystallographic estimations. Additionally
236 5vnx 3qhx Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases 2020 SC Gayathri, N Manoj- Journal of Molecular Biology, 2020 - Elsevier Previously, we reported the biochemical characterization and the crystal structure of an archaeal type-I transferase superfamily and displays the characteristic three-domain architecture of the PLP aldehyde bound form (apoMjDCPLP ALD , non-covalently bound, PDB ID: 3F9T
237 3o2e - Sinorhizobium meliloti YrbA binds divalent metal cations using two conserved histidines 2020 T Roret, G Alloing, JM Girardet, T Perrot- Bioscience, 2020 - portlandpress.com protein structures found in the protein databank, we tentatively attributed the changes to the Interestingly, a structure of a BolA_H from the pathogen Coxiella burnetii ligating a Co atom was solved in the frame of a structural genomic initiative for drug design, deposited in ...The coordinates of A. thaliana, B. bovis, and C. burnetii BolA proteins are from previous crystal structures (PDB entries 4PUG, 4PUH, 4PUI, 3O2E and 3TR3)
238 6n41 - Whole-genome sequencing reveals origin and evolution of influenza A (H1N1) pdm09 viruses in Lincang, China, from 2014 to 2018 2020 XN Zhao, HJ Zhang, D Li, JN Zhou, YY Chen, YH Sun- PloS one, 2020 - journals.plos.org We searched and obtained the model template ( PDB ID: 6n41 .1.A) of HA protein of A/California/07/2009. We conducted a structure prediction of the trimeric HA protein by SWISS-MODEL, then the changes at the epitopes and RBSs were visualized in PyMol
239 3ek1 4o5h Cell-Free Enabled Bioproduction and Biological Discovery 2020 DC Garcia - 2020 - trace.utk.edu The combined use of bioinformatic software and structural data has crystal structures or computationally modeled structures to further cull the listed Enzymatic steps are written above the colored arrows and names of ligands and products underneath their molecular structure
240 4em6 - Metabolomics coupled with SystemsDock reveal the protective effect and the potential active components of Naozhenning granule against traumatic brain injury 2020 J Cao, Y Duan, Y Liu, H Liu, C Wei, J Wang- Journal of, 2020 - Elsevier Orthogonal projection to latent structure -discriminate analysis (OPLS-DA) was also applied to maximize the Compounds, Docking score(> 6.0), Proportion of protein(%), PDB entry, Source 47.2, 4JYU, 4BBE, 1GJO, 3GJS, 4UI1, 2OOW, 4JC1, 5XSR, 1X9D, 6EYI, 4EM6 , 1TJJ, 2OC2
241 3iew 3k2x Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery 2020 AE Wakefield, C Yueh, D Beglov- Journal of Chemical, 2020 - ACS Publications Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for te...
242 4wi1 - Phytochemical, biological and computational investigations of Erythrina fusca Lour. to assess antimalarial property against Plasmodium falciparum 2020 SA Sazed, O Islam, SL Bliese, MRH Hossainey - 2020 - preprints.org All these sub structures impose a chemical structure that has a resemblance only with phaseolin Phaseolin) was subjected to molecular docking study against various proteins of Pf (4plz, 4qt2,4r1e, 4r6w, 4wi1 , 4zxg, 5e16, 5jaz, 5k8s, 5znc, 6aqs, 6ee4, 6fba and 6i4b pdb id
243 4wgj - Bartonella effector protein C mediates actin stress fiber formation via recruitment of GEF-H1 to the plasma membrane 2020 S Marlaire, C Dehio- BioRxiv, 2020 - biorxiv.org On the 130 structural level, BepC displays the ancestral FIC-OB-BID architecture . However, 131 replacement of an acidic residue (D/E) by a lysine (K). The crystal structure of the 134 the - and -phosphates of the ATP analog ( PDB : 4WGJ ), thus functionally replacing 137
244 3oc6 - Characterizing the Fused TvG6PD:: 6PGL Protein from the Protozoan Trichomonas vaginalis, and Effects of the NADP+ Molecule on Enzyme Stability 2020 L Morales-Luna, B Hernndez-Ochoa- International journal of, 2020 - mdpi.com This report describes a functional and structural analysis of fused glucose-6-phosphate dehydrogenase dehydrogenase-phosphogluconolactonase protein from the protozoan Trichomonas vaginalis (T. vaginalis). The glucose-6-phosphate dehydrogenase (g6pd) gene ... Structural superposition of the 6PGL crystal structure from Mycolicibacterium smegmatis MC2 155 (PDB entry 3OC6, steel blue) with the C-terminal 6PGL region of the TvG6PD::6PGL model (spring green).
245 5dd7 - Structural and inhibition studies of thiamine monosphosphate kinase from Mycobacterium tuberculosis 2020 LS Dlamini - 2020 - repository.up.ac.za OT Oxythiamine PDB Protein data bank 38 Figure 3.5: Crystal structure of MtbThiL homodimer ..... 40 bind to both free enzyme and the ES complex. Detailed structural information particularly high resolution crystal structures of substrate
246 3obk - The Se S/N interactions as a possible mechanism of -aminolevulinic acid dehydratase enzyme inhibition by organoselenium compounds: a computational study 2020 PA Nogara, L Orian, JBT Rocha- Computational Toxicology, 2020 - Elsevier Figure 1. (A) The structural formula of some organoselenium compounds, (B) the 5-aminolevulinic acid (5 theory (DFT) approach, are frequently used in the study of structures , reactions, and modeling has been successfully employed to predict the 3D protein structure , which is... (HEM2_STAAR); Toxoplasma gondii: PDB (3OBK); Wolbachia: NCBI (WP_041571452.1).
247 4dz4 - Elucidao estrutural da especificidade por substratos de enzimas da biossntese de aminoglicosdeos e marginolactonas 2020 TP Cardoso - 2020 - repositorio.unesp.br Marginolactone. Structure . Page 9. Lista de Ilustraes AERUGINOSA: GPUA- Q9I6K2; S. CLAVULIGERUS: PAH - P0DJQ3; B. THAILANDENSIS: BUR- Q2T3W4 [ 4DZ4 CDIGO DO PDB ]; D.RADIODURANS: DR_AGM- Q9RZ04; B. CALDOVELOX
248 6bfu - Cryo-electron microscopy structure of the swine acute diarrhea syndrome coronavirus spike glycoprotein provides insights into evolution of unique coronavirus spike 2020 H Guan, Y Wang, V Perulija, AFUH Saeed- Journal of, 2020 - Am Soc Microbiol HCoV-NL63 ( PDB accession number 5SZS); (C) S trimer of the deltacoronavirus PdCoV ( PDB accession number 6BFU ); (D) S bronchitis virus (IBV) ( PDB accession number 6CV0); (E) S trimer of the betacoronavirus SARS-CoV ( PDB accession number 5X58 (F) Structure of the
249 6c9e - Molecular and shell biologyexamining the biochemistry and physiology of prokaryotic nanocompartments 2020 RJ Nichols - 2020 - escholarship.org (B) Size comparison of the nanocompartments to GFP [ PDB : 1C4F], the HK97 viral capsid [ PDB : 1OHG], and the Lastly, given that there is no known structure of a DyP- packaging encapsulin, these nanocompartments may have a pore architecture that permits transit
250 6bfu - Unraveling virus relationships by structure-based phylogenetic classification 2020 WM Ng, AJ Stelfox, TA Bowden- Virus Evolution, 2020 - academic.oup.com Unraveling virus relationships by structure -based phylogenetic classification. Weng M Ng. Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford. ... human coronavirus NL63 (3KBH); human coronavirus 229E (6ATK); porcine deltacoronavirus, PDCoV (6BFU). All chains not comprising S1-CTD (e.g. receptor and antibody fragments) were removed prior to structural alignment
251 6tys - Planejamento de protenas imunognicas multi-eptopo visando o desenvolvimento de uma vacina de nova gerao para a infeco do vrus Nipah 2020 JMP GALCIO - 2020 - repositorio.ufopa.edu.br -defensin adjuvants were also added to the structural models to increase immunogenicity The interactions between each predicted epitope and MHC-I and MHC- II structures were also analyzed, using molecular modeling P Fosfoprotena PDB Protein Data Bank
252 3hgb - Mechanism-driven metabolic engineering for bio-based production of free R-lipoic acid in Saccharomyces cerevisiae mitochondria 2020 B Chen, JL Foo, H Ling, MW Chang- Frontiers in bioengineering and, 2020 - frontiersin.org is glycine cleavage system protein H from Mycobacterium tuberculosis ( PDB chain id: 3hgb .1.A domains) were modeled due to the lack of templates with crystal structure of full acetyltransferase component of the pyruvate dehydrogenase complex in Homo sapiens ( PDB
253 6q06 3sia Host Receptors of Influenza Viruses and CoronavirusesMolecular Mechanisms of Recognition 2020 N Sriwilaijaroen, Y Suzuki- Vaccines, 2020 - mdpi.com A CoV structure with S and HE spikes and positions of S1-NTD and S1-CTD on the S IAVs from avians, either wild birds or domestic birds, typically prefer the 2, 3Sia terminal This representative viral HA is from pdb ID of 3ube, which showed a 2009 pandemic HA in complex... Side view of a surface diagram of a trimeric CoV S protein (pdb: 6q06 [148])
254 6vju - A novel deep-sea bacterial threonine dehydratase drives cysteine desulfuration and hydrogen sulfide production 2020 N Ma, Y Sun, W Zhang, C Sun- bioRxiv, 2020 - biorxiv.org of psTD with mutation of R77E (R is mutated to E; PDB 7DAR) was also solved for 156 comparison 1P5J, 6VJU (1P5J: Ser dehydratase, 6VJU : Cys synthase), which is directly opened to 193 methods. Based on the structure of psTD, its mutant and complex with PLP, we 231
255 6nae - Two Achilles' Heels of the Ebolavirus Glycoprotein? 2020 W Li - 2020 - preprints.org in complex with a broadly neutralizing human antibody, adi-15946 31 6NAE Crystal Structure Structure of ZEBOV GP in complex with 3T0265 antibody 36 6S8J Structure of ZEBOV 1. Experimentally determined Ebolavirus GP structures inside Protein Data Bank ( PDB [128]) as
256 6vxx - Comparative molecular docking analysis of the SARS CoV-2 Spike glycoprotein with the human ACE-2 receptors and thrombin 2020 P Bhanu, NH Kumar, SH Kumar, M Relekar- , 2020 - ncbi.nlm.nih.gov PDB ID, Ligand, Binding Pose, Binding Energy (Kcal/mol), RMSD, Receptor, Bond Length ( Figure 1a: Structural representation of 6VXX and thrombin, Figure 1b: Molecular interaction of with the 7th pose, Key - the sticks represents thrombin, the secondary structure represents the
257 6d8w - Molecular insights into evolution, mutations and receptor-binding specificity of influenza A and B viruses from outpatients and hospitalized patients in 2020 FX Ivan, X Zhou, SH Lau, S Rashid, JSM Teo- International Journal of, 2020 - Elsevier Structural analyses of receptor-binding specificity Then, sialotrisaccharide 3'SLN and 6'SLN isolated from co-crystallized HA-ligand structures in Protein Data Bank ( PDB ) were respectively used as the avian and human receptor analogs to assess receptor-binding
258 5eks - Structural and biochemical analyses reveal that chlorogenic acid inhibits the shikimate pathway 2020 N Neetu, M Katiki, A Dev, S Gaur, S Tomar- Journal of, 2020 - Am Soc Microbiol replacement method using the coordinates of chain A of DHQS enzyme from Vibrio cholerae ( PDB identifier [ID]: 3OKF Structural comparison of PaDHQS structure with its homologs closer to its homologs from A. nidulans (1SG6), V. cholerae (3OKF), A. baumannii ( 5EKS ), and H
259 3dmp 3hm0, 3e5b, 3qbp Tetramer protein complex interface residue pairs prediction with LSTM combined with graph representations 2020 D Sun, X Gong- Biochimica et Biophysica Acta (BBA)-Proteins and, 2020 - Elsevier The structure diagram of LSTM neural network is shown in Fig. 3. (See Fig. 1, Fig Table 1. Dataset. DataSet, PDB ID 2H8N, 2JBR, 2NQO, 2Y32, 3DFQ, 3ESI, 3G7K, 3HM0, 3OHP, 3RD4, 3 V15, 1IZ1, 1JL2. 1KAM, 1NSW, 2GJD, 2R90, 2ZYZ, 3CDK, 3CO2, 3DMP , 3F6Z, 1BV4, 1YIF
260 5td3 5umh, 5vxt Characterization of a Novel Functional Trimeric Catechol 1, 2-Dioxygenase From a Pseudomonas stutzeri Isolated From the Gulf of Mexico 2020 J Rodrguez-Salazar, AG Almeida-Juarez- Frontiers in, 2020 - frontiersin.org substrates in its catalytic site (Vetting and Ohlendorf, 2000; Earhart et al., 2005; Micalella et al., 2011, PDB entries: 2XSR 5UMH, 5TD3 , and 5VXT) model of PSC12DO was elaborated using the CPHmodels 3.2 Server based on the C12DO P. arvilla structure (PDBid: 2AZQ ... Burkholderia vietnamiensis, 48% (PDBid:5TD3); and Burkholderia ambifaria, 43% (PDBid:5VXT). The most variable regions are located in residues 1–29
261 3i4e 3p0x Biochemical properties and crystal structure of isocitrate lyase from Bacillus cereus ATCC 14579 2020 SH Lee, D Ki, S Kim, IK Kim, KJ Kim- Biochemical and Biophysical, 2020 - Elsevier 2.5. Structure determination of BcICL. The structure of BcICL was determined using the molecular replacement method with the CCP4 version of MOLREP [24]. The structure of Isocitrate lyase from Burkholderia pseudomallei ( PDB code 3I4E ) was used as a search model
262 6bfu - A thermostable, closed SARS-CoV-2 spike protein trimer 2020 X Xiong, K Qu, KA Ciazynska, M Hosmillo- Nature Structural &, 2020 - nature.com Structures of the disulfide-stabilized and non-disulfide-stabilized proteins reveal distinct closed and locked conformations of the S trimer with the target cell, and is a dominant target of the immune system 4 . S protein is trimeric and has two distinct structural statesprefusion ... porcine deltacoronavirus (PDCoV, a deltacoronavirus, PDBID: 6BFU). S proteins are structurally aligned based on S2. S protein trimers from all 4 genera of
263 3krs - Gene Cloning, Recombinant Expression, Characterization, and Molecular Modeling of the Glycolytic Enzyme Triosephosphate Isomerase from Fusarium oxysporum 2020 B Hernndez-Ochoa, S Gmez-Manzo- Microorganisms, 2020 - mdpi.com Triosephosphate isomerase (TPI) is a glycolysis enzyme, which catalyzes the reversible isomerization between dihydroxyactetone-3-phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP). In pathogenic organisms, TPI is essential to obtain the energy used to survive and infect ... Figure 2. Bioinformatic analysis of FoxTPI with other triosephosphate isomerases (TPIs)... , 3KRS (Cryptosporidium Parvum), 5UPR (Toxoplasma gondii),
264 6nb3 6vxx, 6vyb, 6nb6, 6nb4, 6nb7 Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel 2020 I Mercurio, V Tragni, F Busto, A De Grassi- Cellular and Molecular, 2020 - Springer Download PDF. Download PDF. Original Article; Published: 04 July 2020. Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies
265 3laa 3s6l, 4lgo Non-adaptive evolution of trimeric autotransporters in Brucellaceae 2020 MR Rahbar, M Zarei, A Jahangiri, S Khalili- Frontiers in, 2020 - ncbi.nlm.nih.gov domain from Haemophilus influenzae genome ( PDB ID:1S7M; Yeo et al., 2004); structure of the parallel beta-roll collagen-binding domain of Yersinia enterocolitica adhesin YadA ( PDB ID: 1P9H Batch analyzes of the dataset suggested the existence of a few structural domains
266 6q05 - Evaluation of Coronavirus families & Covid-19 proteins: molecular modeling study 2020 M Monajjemi, S Shahriari- Biointerface Res. Appl, 2020 - biointerfaceresearch.com Several Proteins, receptors, S proteins including s1 and s2 such as 6LU7, 6Q05 , 4oW0, 6nur The Structure Preparation modules of MOE were used to correct PDB inconsistencies and to assign the structural knowledge of the CoV-RNA synthesis complexes was a structure of the
267 6nb6 - SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics 2020 R Gupta, J Charron, CL Stenger, J Painter- Journal of Biological, 2020 - Elsevier receptor structure -function. post-translational modification (PTM). COVID-19. severe acute respiratory coronavirus 2 (SARS-CoV-2) Their 2633-kb genome consists of positive-sense, single-stranded RNA, coding for nonstructural and structural proteins This protein complex model was built through the integration of PDB structures 6CRW, 6NB6, and 5X58 for the trimer of spike proteins with 6M17,
268 6wpt - The SARS-CoV-2 spike glycoprotein as a drug and vaccine target: Structural insights into its complexes with ACE2 and antibodies 2020 AC Papageorgiou, I Mohsin- Cells, 2020 - mdpi.com 3. S protein Structural Details The reported structure revealed an asymmetric trimer and two conformations for one of the RBDs: up and down (Figure 3). The ACE2 binding was recently investigated in more detail, resulting in ten structures with the RBDs at different stages of ... Cryo-Electron Microscopy (Cryo-EM) structure of S309 antibody with the S glycoprotein trimer (PDB id 6wpt). The antibody chains are colored in cyan (L chain) and cornflower blue (H chain)
269 6nb7 6ws6, 6wpt, 6wps, 6nb8 Structural basis of SARS-CoV-2 and SARS-CoVantibody interactions 2020 E Gavor, YK Choong, SY Er, H Sivaraman- Trends in, 2020 - Elsevier While the binding of COV21 to the S-glycoprotein resembles the binding of the SARS-CoV S230( PDB : 6NB7 )[73], the binding interface SARS-CoV-2-S-S309-Fab[12] complex ( PDB : 6WPS/6WPT/6WS6) and the crystal structure of SARS
270 3jst - Role of tetrachloro-1, 4-benzoquinone reductase in phenylalanine hydroxylation system and pentachlorophenol degradation in Bacillus cereus AOA-CPS1 2020 OA Aregbesola, A Kumar, MP Mokoena- International Journal of, 2020 - Elsevier Three-dimensional structure and homology modelling of the protein were predicted by submitting the amino acid sequence at the SWISS-MODEL tool at The modelled PDB files were submitted to an online tool (PDBsum) for determining the structural summary [34]. 2.12 ... and sequence identity of 59%, followed by PCD/DCoH (PDB: 3JST) from Brucella melitensis,
271 3sdo - On the diversity of F420-dependent oxidoreductases: a sequence-and structure-based classification 2020 ML Mascotti, MJ Ayub, M Fraaije- bioRxiv, 2020 - biorxiv.org monooxygenase (NTA_MO, PDB : 3sdo ), as well as the well-known bacterial FMN- dependent luciferases (eg.: LuxB, PDB : 1luc) [28]. The topology suggests that cofactor vary considerably in structure and function, and comprise the F420H2-NADP+ oxidoreductases
272 6ona - Evolution of H9N2 avian influenza viruses in Iran, 20172019 2020 M Bashashati, DH Chung- Transboundary and, 2020 - Wiley Online Library (http://www.cbs.dtu.dk/services/NetNGlyc/) and GlyProt server (http://www.glycosciences.de/ modeling/). The HA structure was modelled using the H9 HA template ( PDB accession number, 6ONA ) in the SWISS-MODEL server (https://swissmodel.expasy.org/) and
273 4y0e - Pathway from Nalkylglycine to alkylisonitrile catalyzed by iron (II) and 2oxoglutarate dependent oxygenases 2020 WC Chang, TY Chen, J Chen, Y Tang- Angewandte, 2020 - Wiley Online Library Table S4). Dali search suggested the structure of ScoE resembles those of other Fe/2OG-enzymes such as CarC ( PDB ID: 4oj8) and a putative dioxygenases ( PDB ID: 4y0e ), with Z-score of 20.0 and 26.7, respectively. In the
274 3uam - Characterization of a bacterial copperdependent lytic polysaccharide monooxygenase with an unusual second coordination sphere 2020 A Munzone, B El Kerdi, M Fanuel- The FEBS, 2020 - Wiley Online Library by a glycine instead [23,24,26]. Additionally, a crystal structure of a putative AA10 LPMO from Burkholderia pseudomallei with a methionine in place of the alanine was released in the Protein Data Bank ( PDB accession code 3UAM )
275 6an0 - The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes 2020 S Del Duca, S Chioccioli, A Vassallo, LM Castronovo- Microorganisms, 2020 - mdpi.com 6AN0 Elizabethkingia anophelis Amino acid sequences from HisA/HisF, IGPD, and HDH, available in the PDB , were downloaded from UniProt [29], aligned using BioEdit [30] through the ClustalW tool [31], and the conservation of the secondary structure organization was
276 3gka - Two new ene-reductases from photosynthetic extremophiles enlarge the panel of old yellow enzymes: CtOYE and GsOYE 2020 MS Robescu, M Niero, M Hall, L Cendron- Applied Microbiology, 2020 - Springer The most peculiar structural features of each enzyme are depicted in bright orange (loop 3 In the active site of GsOYE structure , a chloride anion, present in the crystallization In the structures of the GsOYE complexes, both para-hydroxybenzaldehyde (pHBA; PDB : 6S31) (Fig
277 6c9e - Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism 2020 RJ Nichols, B LaFrance, NR Phillips, LM Oltrogge- bioRxiv, 2020 - biorxiv.org additional density for the holo-SrpI with a 243 homologous cysteine desulfurase dimer docked in ( pdb : 6c9e ) the first Family 2 encapsulin structure and is 267 the highest resolution structure for an Given the structural 271 similarity of the entire shell, it is unsurprising that the SrpI
278 3h7f - Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling 2020 JMH Thomas, RM Keegan, DJ Rigden- Section D: Structural, 2020 - scripts.iucr.org This led to the solution of five new structures ( PDB entries 2v71, 3cvf, 3h7f , 3mqc and 3trt) in As an example, PDB entry 3mqc failed to solve using default models (Fig 3b), through an ensemble that included substantial common helical structure with deviation at either end (Fig
279 3cez 3cxk Structure and Electron-transfer Pathway of the Human Methionine Sulfoxide Reductase MsrB3 2020 G Javitt, Z Cao, E Resnick, R Gabizon- and Redox Signaling, 2020 - liebertpub.com MsrB3 molecules per asymmetric unit. The structure was solved by molecular replacement using a bacterial MsrB protein ( PDB code 3CEZ ) with high sequence identity to human MsrB3 (74 of 119 residues, or 62%) (6). Though the amino-terminal segment containing
280 3rr6 4maq, 4pfz, 3qdf Sequence, structure and functionbased classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies 2020 H Hong, H Seo, W Park, KJ Kim- Environmental microbiology, 2020 - Wiley Online Library This article is protected by copyright. All rights reserved. Page 24. uncharacterized protein from M. abscessus DSM 44196 ( PDB code 3RR6 , 36 % sequence identity) as a search model. The structure model was built using the WinCoot program (Emsley
281 4yl5 - Essential Metabolic Routes as a Way to ESKAPE from Antibiotic Resistance 2020 ALC Barra, CD Lvia de Oliveira, LG Moro- Frontiers in Public, 2020 - ncbi.nlm.nih.gov ID 2I5B (23)], Thermus thermophilus ( PDB ID 1UB0), A. baumannii ( PDB ID 4YL5 ), Bacteroides thetaiotaomicron tuberculosis (3O63), and for the bifunctional enzyme from Candida glabrata [ PDB IDs 3NL2 No crystal structure of an ESKAPE pathogen, ThiE, is available to date
282 6nb6 - Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing 2020 T Desautels, A Zemla, E Lau, M Franco, D Faissol- BioRxiv, 2020 - biorxiv.org In the absence of a known SARS-CoV-2 spike protein structure , we characterized the SARS-CoV- 2 surface glycoprotein sequence YP_009724390.1 [13 The structures of the spike proteins from SARS-CoV-1 (Protein Data Bank ( PDB ) entries: 5x58 [15], 6nb6 [10], 2dd8 [11
283 2lwk - DrugPred_RNAStructure-based druggability predictions for RNA binding sites 2020 IH Rekand, R Brenk - 2020 - chemrxiv.org However, the structure of the complex has been determined by NMR and it is possible that the resolution of the structure is not accurate enough to reveal the actual details of the binding mode.51 The Spinach Figure 6: Binder of influenza A promoter region ( PDB ID 2lwk )
284 4qji - Natural products encompassing antituberculosis activities 2020 A Monga, A Sharma- Studies in Natural Products Chemistry, 2020 - Elsevier The structure and composition of the cell envelope of M. tuberculosis are distinguished from that of other kinds of prokaryotes S. No. PDB ID, Title, Anti-TB agents 1OY0, Pantothenate kinase, 1e. 4QJI , Phosphopantothenate-cysteine ligase, Phosphopantetheine
285 5cy4 - A functional and structural study of three bacterial nucleic acid-interacting proteins. The story of a Ferric Uptake Regulator, an Oligoribonuclease and an ATP 2020 K Berg - 2020 - munin.uit.no Acinetobacter baumannii (PDB 5CY4) and E. coli (PDB code 1YTA )[148]. All Orn homologs are structurally similar and topologically arranged
286 6nb7 - Molecular Modelling and Docking Experiments Examining the Interaction between SARS-CoV-2 Spike Glycoprotein and Neuronal Nicotinic Acetylcholine Receptors 2020 K Farsalinos, E Eliopoulos, D Leonidas - 2020 - preprints.org receptor ( PDB id: 6NB7 ) and the extracellular domain of the nAChR alpha9 subunit in complex with alpha-bungarotoxin ( PDB id: 3U8M) were downloaded from the Protein Data solved yet, we used the crystal structure of the extracellular domain of the homologous
287 3t7c 3pgx Identification of Genes Involved in IN VIVO Virulence of Mycobacterium Fortuitum as Potential Drug Target 2020 R Srivastava - 2020 - ir.juit.ac.in acidic, hypoxic and detergent stress conditions. Structural and functional characterization of most potent ORF Mfsdr was done using in silico approaches. MfSdr was predicted to be acid synthesis. Secondary structure of MfSdr generated using Robetta server showed presence
288 4ohc - Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by means of X-ray Crystallography and Computational Simulations 2020 M Roca, S Navas-Yuste, K Zinovjev- ACS, 2020 - ACS Publications Then, the dimeric architecture of OPRTase plays an essential role in the catalysis since The coordinates and structure factors have been deposited in the Protein Data Bank ( PDB ) with accession codes 6TAI (EcOPRT), 6TAJ (EcOPRT/OA) and 6TAK (EcOPRT/OA/SO4 2-). 2.5
289 3u0g - Structural insight into the substrate specificity of PLP fold type IV transaminases 2020 EY Bezsudnova, VO Popov, KM Boyko- Applied Microbiology and, 2020 - Springer Due to the rigid structure of the -sheet, the residues constituting it form a peculiar mold for substrate binding. The interdomain loop (light blue) and -turn (black) of the large domain of the first subunit confine the P-pocket from the other sides PDB ID:*. X-strand 3U0G
290 4q4l - Design and Synthesis of Near-Infrared Mechanically Interlocked Molecules for Specific Targeting of Mitochondria 2020 RS Das, PC Saha, N Sepay, A Mukherjee- Organic, 2020 - ACS Publications The entrapment of squaraine (SQ) within a molecular container to form rotaxane has been shown to improve the dye stability and the fluorescence proficiency inside the mitochondria. The macrocycle p... The molecular docking of MSQ with Cys exposed mitochondrial protein ATP synthase subunit beta 1 (PDB: 4Q4L), and other SH-exposed proteins showed interactions between the SH moieties and MSQ
291 3sw5 3fq3 Effect of Structure Variations in the Inter-subunit Contact Zone on the Activity and Allosteric Regulation of Inorganic Pyrophosphatase from Mycobacterium tuberculosis 2020 RS Romanov, SA Kurilova, AA Baykov- Biochemistry (Moscow, 2020 - Springer of Ec PPase [15, 16], and bound L malate was found in the crystal struc ture of PPase from Bartonella henselae ( PDB ID 3SW5 ) Furthermore, modification of the subunit contact zones does not change the oligomeric structure of Mt PPase, but makes it less compact, as shown
292 6q04 - An overview of Middle East respiratory syndrome coronavirus vaccines in preclinical studies 2020 N Zhang, J Shang, C Li, K Zhou, L Du- Expert Review of Vaccines, 2020 - Taylor & Francis Structures of MERS-CoV S1-NTD and MERS-CoV S1-NTD-Neu5Ac complex are presented by ribbon model ( PDB code 6Q04 ) (A) Structure of MERS Both MERS-CoV macro domain and ADP-ribose are presented by ribbon model in green and red, separately ( PDB code 5DUS
293 3u04 - Drug Repurposing in Cancer Therapy: Approaches and Applications 2020 KKW To, WCS Cho - 2020 - books.google.com Page 1. Drug RE pu irposir g in Approaches and Applications Edited by Kenneth K. W. To William CS Cho MEDIA BUSINESS WORLD TUORK $60CM WORLD so OH HC E ENT N-Cro C CI AP CH3 Page 2. DRUG REPURPOSING IN CANCER THERAPY Page 3
294 3cez - On the functionality of a methionine sulfoxide reductase B from Trypanosoma cruzi 2020 DG Arias, MS Cabeza, ML Echarren- Free Radical Biology, 2020 - Elsevier These enzymes can reduce specifically one or another of the isomers of MetSO (free and protein-bound). This redox modification could change the structure and function of many proteins, either concerned in redox or other metabolic pathways ... Models were based on the resolved structure of MSRB from Methanothermobacter thermautotrophicus (PDB 2K8D), Burkholderia pseudomallei (PDB 3CEZ), and Xanthomonas campestris (PDB 3HCI).
295 6vxx 6vyb Glycans on the SARS-CoV-2 spike control the receptor binding domain conformation 2020 R Henderson, RJ Edwards, K Mansouri, K Janowska- bioRxiv, 2020 - ncbi.nlm.nih.gov this map yielding a structure aligning to the unmutated 2P structure ( PDB ID 6VXX ) with a one RBD 'up' state structure fit to this map to its unmutated counterpart ( PDB ID 6VYB N234A mutation (Figure 3E and andF).F). However, the limited resolution of this structure limits close
296 6nb6 - Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein 2020 X Fan, D Cao, L Kong, X Zhang- Nature communications, 2020 - nature.com However, structural information of the post-fusion S2 from these highly pathogenic human-infecting The structures of pre- and post-fusion SARS-CoV S glycoprotein dramatically differ This structure suggests potential targets for the development of vaccines and therapies against
297 6q04 6VXX The sialoside-binding pocket of SARS-CoV-2 spike glycoprotein structurally resembles MERS-CoV 2020 M Awasthi, S Gulati, DP Sarkar, S Tiwari, S Kateriya- Viruses, 2020 - mdpi.com Multiple sequence alignment of the NTD domains was performed with the Clustal W program [15]. 2.2. Structure Prediction. The cryo-EM structures of SARS-CoV-2 ( PDB ID: 6VXX) [8] and MERS-CoV ( PDB ID: 6Q04 ) [11] spike glycoproteins were used as the starting point for
298 5j3b - Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System 2020 MB Bertelsen, M Senissar, MH Nielsen, F Bisiak- Structure, 2020 - Elsevier Here, we provide structural insights into the architecture of the intact VapXD TA complex and toxin residues missing in each chain likely due to flexibility (Figure S1A). The structure consists of PDB Entry, VapXD (Selenomethionine) 6ZN8, VapD (Wild Type) 6ZI0, VapD (D7N) 6ZI1... (B) Structure of the Acinetobacter baumannii EF-P OB fold with conserved secondary structure in gold (PDB: 5J3B, left) and corresponding topology (right).
299 3cxk - Functional characterization of methionine sulfoxide reductases from Leptospira interrogans 2020 N Sasoni, MD Hartman, SA Guerrero- et Biophysica Acta (BBA, 2020 - Elsevier The Met oxidation could change the structure and function of many proteins, not only of those redox-related but also of others involved in different metabolic pathways. Until now, there is no information about the presence or function of Msrs enzymes in Leptospira interrogans
300 5dld 4hwg UDP-N-acetilglicosamina 2-epimerase de Staphylococcus aureus: estrutura, dinmica e prospeco de novos ligantes 2020 C Azevedo - teses.usp.br the crystallographic structure of the enzyme to characterize conformational changes as they 45 Figura 13 Estrutura cristalogrfica da cadeia A da protena UDP-GlcNac 2-epimerase de S. aureus ( PDB : 5ENZ), com uma molcula de UDP em stio ativo, vista de frente (A) e
301 3v7o 5dvw Crystal structure of the Mngl virus VP30 C-terminal domain 2020 S Dong, K Wen, H Chu, H Li, Q Yu, C Wang- and Biophysical Research, 2020 - Elsevier VP30 CTD dimers formed from adjacent crystallographic asymmetric units with those of MARV ( PDB code: 5T3W), RESTV ( PDB code: 3V7O ) and EBOV ( PDB code: 5T3T) In this study, we determined the crystal structure of MLAV VP30 CTD monomer at 1.4 resolution
302 4odj - Engineered SAM synthetases for enzymatic generation of AdoMet analogs with photocaging groups and reversible DNA modification in cascade reactions 2020 F Michailidou, N Klcker- Angewandte Chemie, 2020 - Wiley Online Library Figure 3. A) Superimposed structures of WT-ChMAT ( 4ODJ , shown in yellow) with product bound PC-ChMAT (6LTV, shown in grey) and share a sequence identity of 51% and are highly conserved in the active site (Figure S17), and our structure of PC-ChMAT ( PDB ID: 6LTV
303 3ujh - When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina 2020 Y Li, S Mohanty, D Nilsson, B Hansson, K Mao- Scientific reports, 2020 - nature.com F. ovina. Using simulated native-state ensembles, we examine the structural properties and binding tightness of the dimers. In addition, we investigate their ability to withstand dissociation when pulled by a force. Our results
304 5vog - ALIXE: a phase-combination tool for fragment-based molecular replacement 2020 C Milln, E Jimnez, A Schuster- Section D: Structural, 2020 - scripts.iucr.org 2.4.1. Hypothetical protein ( PDB entry 5vog ). The crystal structure of a hypothetical protein from Neisseria gonorrhoeae with bound ppGpp was downloaded from the PDB ( PDB entry 5vog ; Seattle Structural Genomics Center for Infectious Disease, unpublished work)
305 5tw7 - Helices on interdomain interface couple catalysis in the ATPPase domain with allostery in Plasmodium falciparum GMP synthetase 2020 S Shivakumaraswamy, N Pandey, L Ballut, S Violot- bioRxiv, 2020 - biorxiv.org Experimental Procedures. Sequence and structure analysis The PDB IDs of the structures of GMPS analyzed are 1GPM (Escherichia coli), 3TQI (Coxiella burnetii), 2YWB and 2YWC (Thermus thermophilus), 5TW7 (Neisseria gonorrhoeae), 2VXO (Homo sapiens), 3UOW
306 6bfu - Structure and immune recognition of the porcine epidemic diarrhea virus spike protein 2020 RN Kirchdoerfer, M Bhandari, O Martini, LM Sewall- bioRxiv, 2020 - biorxiv.org from HuCoV-NL63 (5SZS. pdb (Walls et al., 2016b)), Porcine deltacoronavirus ( 6BFU . pdb , (Xiong et pdb , (Kirchdoerfer et al., 2018)) and Infectious bronchitis virus (6CV0. pdb , (Shang et the PEDV spike differs in several regards to the previously determined NL63 spike structure
307 3qi6 6cja Catalytic specificity of the Lactobacillus plantarum cystathionine -lyase presumed by the crystallographic analysis 2020 Y Matoba, M Noda, T Yoshida, K Oda, Y Ezumi- Scientific Reports, 2020 - nature.com The reverse transsulfuration pathway, which is composed of cystathionine -synthase (CBS) and cystathionine -lyase (CGL), plays a role to synthesize l-cysteine using l-serine and the sulfur atom in l-methionine. A plant-derived lactic acid bacterium Lactobacillus plantarum SN35N
308 4k9d - Network-Pharmacology and DFT Based Approach Towards Identification of Leads from Homalomena aromatica for Multi-Target In-Silico Screening on Entamoeba 2020 AK Goswami, HK Sharma, N Gogoi- Current Drug, 2020 - ingentaconnect.com The 3D model of EhGAPDH was predicted based on multiple templates ( PDB IDs: 4O59, 4K9D , 1U8F, 4Z0H, 3V1Y) It uses robust, cross-validated Quantitative Structure Toxicity Relationship (QSTR) models for assessing various measures of toxicity. 3.6
309 6wps 6wpt Immunological strategies against spike protein: Neutralizing antibodies and vaccine development for COVID19 2020 J Huang, H Huang, D Wang, C Wang- Clinical and, 2020 - ncbi.nlm.nih.gov Structural data of RBD of SARSCoV2 S protein with CR3022 Fab was retrieved from Protein Databank. (C) Structure of SARSCoV2 S protein with neutralizing antibody S309 Fab fragment ( PDB : 6WPS ) is shown in close state
310 3eiy - Graphein-a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures 2020 AR Jamasb, P Li, T Blundell- bioRxiv, 2020 - biorxiv.org Figure 1. Example outputs from Graphein. A Example protein surface ( 3eiy ). B Example node feature matrix for the residue-level graphs outlined The interaction status data and structure originate from structures of the complexes in the RCSB PDB
311 2lwk - Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting 2020 M Bissaro, M Sturlese, S Moro- Frontiers in Chemistry, 2020 - frontiersin.org (B) Superimposition between the experimental NMR complex ( PDB ID 2LWK , green-colored DPQ (D) RMSD of RNA phosphate atoms belonging to the backbone, computed against the PDB reference. (E) Flexibility characterizing the RNA structure during DPQ binding event
312 4ot8 - l-Threonine Transaldolase Activity Is Enabled by a Persistent Catalytic Intermediate 2020 P Kumar, A Meza, JM Ellis, GA Carlson- ACS Chemical, 2020 - ACS Publications l-Threonine transaldolases (lTTAs) are a poorly characterized class of pyridoxal-5-phosphate (PLP) dependent enzymes responsible for the biosynthesis of diverse -hydroxy amino acids... The structure was solved by molecular replacement with a distantly related serine hydroxymethyltransferase (PDB ID: 4OT8, 28.2% identity
313 5ez3 - Characterization of sulfated polysaccharide activity against virulent Plasmodium falciparum PHISTb/RLP1 protein 2020 JM Mutisya, VA Mobegi, JK Kinyua, MN Kivecu- , 2020 - f1000research.com sequences to the reference, 12 non-synonymous single nucleotide polymorphisms were considered for mutant protein structure analysis. Eleven drug compounds with antiplasmodial activity were identified. Both modelled PHISTb/RLP1 reference and mutant structures had a
314 5i1f 5ve7, 5vct, 5j49 In vitro and in vivo Evaluation of in silico Predicted Pneumococcal UDPG: PP Inhibitors 2020 F Cools, D Triki, N Geerts, P Delputte- Frontiers in, 2020 - frontiersin.org Currently, the crystal structure of UDPG:PP is only known for several eukaryotes and following bacteria: Helicobacter pylori ( PDB codes 3JUJ and 3JUK) (Kim et al., 2010), E. coli ( PDB code 2E3D) (Thoden and Holden ( PDB codes 5VCT, 5VE7, 5J49, 5I1F ) (Abendroth et al
315 6nb6 - Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies 2020 CO Barnes, AP West Jr, KE Huey-Tubman- Cell, 2020 - Elsevier Share. Export. Advanced. Cell Cell. Volume 182, Issue 4, 20 August 2020, Pages 828-842.e16. Journal home page for Cell. Article. Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies
316 6q06 - Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection 2020 J Fantini, C Di Scala, H Chahinian, N Yahi- International journal of, 2020 - Elsevier N-acetylneuraminic acid (Neu5Ac) was generated with the Hyperchem database. 9-O-acetyl-N-acetylneuraminic acid (9-O-SIA) was retrieved from pdb file 6Q06 [18] Its three-dimensioanl structure was retrieved from pdb file # 4V2O [19]
317 4g5d - Leishmania braziliensis prostaglandin F 2020 EVC AlvesFerreira, TR Ferreira, P Walrad - 2020 - parasitesandvectors.biomedcentral 1b) and the 3D structure (Fig c 3D sequence alignments of protein sequences of LmjPGF2S (PBD ID 4G5D , in grey) and human ortholog share 51.4% similarity and 34.3% identity, modelling using the Research Collabora- tory for Structural Bioinformatics (RCSB) PDB suggests
318 5upg - Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity 2020 Y Yamada, H Takashima, DL Walmsley- Journal of Medicinal, 2020 - ACS Publications UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is a zinc metalloenzyme that catalyzes the first committed step in the biosynthesis of Lipid A, an essential component of the cell envelope of Gr... Figure 3. Detail of the crystal structure (PDB code: 5UPG) of 1 (PF-5081090) binding to the active site of PaLpxC
319 5dvw - Napovedni modeli za identifikacijo potencialnih inhibitorjev razlinih proteinov virusa ebole 2020 V Hudi - 2020 - core.ac.uk Monte Carlo MLR Multivariatna linearna regresija mRNA Informacijska ribonukleinska kislina NP Nukleoprotein PCA Metoda glavnih komponent PDB Podatkovna knjinica Knowledge of the viral structure gives us insight into the functioning of the virus and allows us to predict
320 3qh4 - Crystal structure of PMGL2 esterase from the hormone-sensitive lipase family with GCSAG motif around the catalytic serine 2020 KM Boyko, MV Kryukova, LE Petrovskaya- PloS one, 2020 - journals.plos.org mPMGL2 demonstrated no structural or biochemical differences compared to the wild type enzyme, but with the atomic coordinates of the esterase EstE5 from uncultured bacterium ( PDB ID: 3L1H The wtPMGL2 structure was then used to solve mPMGL2 at 1.43 resolution... Besides the above mentioned enzymes, the only known structure of an enzyme from the GTSAG subfamily of bHSL is an esterase LipW from Mycobacterium marinum (PDB ID 3QH4), whose proposed dimer also shares the same structural feature
321 5t8s - Prospects of Indole derivatives as methyl transfer inhibitors: antimicrobial resistance managers 2020 S Tha, S Shakya, R Malla- BMC, 2020 - bmcpharmacoltoxicol.biomedcentral An integration of structure -based virtual screening and ligand-based virtual screening was employed to explore the antimicrobial properties of indole The X-ray diffraction structures of S-adenosyl methionine synthase, MetK from N. gonorrhoeae ( PDB id: 5T8S ) [13]; cobA from
322 3gbz - How evolution designs functional free energy landscapes of proteins? A case study on emergence of regulation in CDK family kinases. 2020 Z Shamsi, D Shukla- Molecular Systems Design & Engineering, 2020 - pubs.rsc.org structures of CDK2 ( PDB ID: 5OSM, 6Q3F, 6Q4A, 6Q4B, 6Q4C, 6Q4D, 6Q4K), G/CDK ( PDB ID: 3GBZ ), and pfpk5 structures are native-like based on GA341 score and have comparable DOPE score with CDK2 native structure as shown in PDB ID for CMGI for native CDK2 score
323 6cfp - New anti-viral drugs for the treatment of COVID-19 instead of favipiravir 2020 A Akta, B Tzn, R Aslan, K Sayin- Biomolecular Structure, 2020 - Taylor & Francis According to Table 2, the 6CFP protein is not inhibited by any ligands RNA polymerase proteins with PDB IDs of 6NUR and 6NUS were reported in late 2019 and early In this calculation, the ligand and protein are flexible and solvent molecules surround the entire structure
324 2lwk - Using Machine Learning to Better Predict the Structure of RNA and RNA Containing Complexes 2020 S Chhabra - 2020 - deepblue.lib.umich.edu 53 3.5 Top 10 RNA Structures for 2LWK predicted from sequence using CS-Fold and Rosetta structures . The statistics from Protein Data Bank ( PDB ) (http://www.rcsb.org) current understanding of the RNA structure -function relationships is limited due to
325 6bfu 6nb4 Cryo-electron microscopy structure of the SADS-CoV spike glycoprotein provides insights into an evolution of unique coronavirus spike proteins 2020 S Ouyang- BioRxiv, 2020 - biorxiv.org lower and outer side of S1-CTDs arranged as a big triangle. This architecture , 157 ie, CTD sandwiched by its own NTD and the adjacent NTD, comes into being 158 189 (G). Cryo-EM structure of SADS-CoV S monomeric subunit. The structural 190
326 6wps - Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition 2020 OC Grant, D Montgomery, K Ito, RJ Woods- Scientific reports, 2020 - nature.com The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor Here we examine the structure of the SARS-CoV-2 envelope spike (S) protein that mediates host cell infection, with a. ... However, a closer examination also indicates a contraction between the 3D glycoform model and the observed binding of the neutralizing antibody S309 (PDB ID 6WPS).
327 3tmg - Examination and reconstitution of the glycine betaine-dependent methanogenesis pathway from the obligate methylotrophic methanogen Methanolobus vulcani B1d 2020 AJ Creighbaum - 2020 - rave.ohiolink.edu 18 Active site predictions of DhMtgB and MV8460 76 19 Predicted structural model of MV10350 compared to 78 (Hagemeier et al., 2006). No further crystal structure evidence is available to understand the mechanism of demethylation by MtsA or the enzymes responsible for
328 4kam - Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum 2020 Y Wang, L Fan, P Tuyishime, J Liu, K Zhang- Communications, 2020 - nature.com Synthetic methylotrophy has recently been intensively studied to achieve methanol-based biomanufacturing of fuels and chemicals. However, attempts to engineer platform microorganisms to utilize methanol mainly focus on enzyme and pathway engineering... The model structure of the wild-type Cgl0653 was constructed with the crystal structure of O-acetyl-L-homoserine sulfhydrylase from Mycobacterium marinum ATCC BAA-535 (PDB ID: 4KAM) as a template (54% sequence identity with Cgl0653)
329 6q05 - Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein reveals an evolutionary distinct and proteolytically sensitive activation loop 2020 JA Jaimes, NM Andr, JS Chappie, JK Millet- Journal of molecular, 2020 - Elsevier Volume 432, Issue 10, 1 May 2020, Pages 3309-3325. Journal home page for Journal of Molecular Biology. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop
330 3p0x - Characterisation and structural analysis of glyoxylate cycle enzymes of Teladorsagia circumcincta 2020 S Umair, C Bouchet, N Palevich, HV Simpson- Molecular and Biochemical, 2020 - Elsevier to compare the TciICL and TciMS protein sequences with deposited structures in the Protein Data Bank ( PDB ) Locations are shown of the C- and N-terminus in the predicted tertiary structure of TciICL C) and TciMS in salmon (F) within 4 of the superimposed 3P0X and 3S9Z
331 3eiy - Utilising Graph Machine Learning within Drug Discovery and Development 2020 T Gaudelet, B Day, AR Jamasb, J Soman- arXiv preprint arXiv, 2020 - arxiv.org and evolve along a temporal dimension resulting in changes to composition, structure and attributes One such approach is to use a graph's structural information to regularise embeddings authors suggest the atten- tion mechanism is decoupled from the architecture and should
332 3p96 - Biochemical characterization of phosphoserine phosphatase SerB2 from Mycobacterium marinum 2020 E Pierson, J Wouters- Biochemical and Biophysical Research, 2020 - Elsevier MmaSerB2 and MtbSerB2 are similar in their catalytic behaviour and architecture . Fig. 2. A) Structure of MmaSerB2 modeled by homology on the basis of M. avium SerB structure ( PDB 3P96 ). The individual domains are labelled. Active site residues are shown in red
333 5trw 5tqi Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani 2020 S Are, S Gatreddi, P Jakkula, IA Qureshi- International Journal of Biological, 2020 - Elsevier with ADP pyridoxamine, ADP pyridoxine, ADP ginkgotoxin and ADP alone have also been determined to provide structural insights of The initial phases of LdPdxK-ADP structure were obtained using the coordinates of sheep brain pyridoxal kinase ( PDB code 1LHP; 38
334 3khp - Proteinprotein interaction of Rv0148 with Htdy and its predicted role towards drug resistance in Mycobacterium tuberculosis 2020 G Bhargavi, S Hassan, S Balaji, SP Tripathy- BMC microbiology, 2020 - Springer Rv0148 and Htdy interaction analysis The crystallographically determined structure of Htdy ( PDB code 3KHP ) and the predicted model structure of Rv0148 were used for docking using the ClusPro server b Ramachandran plot for the predicted model structure of Rv0148
335 4xgi - Structural studies of glutamate dehydrogenase (isoform 1) from Arabidopsis thaliana, an important enzyme at the branch-point between carbon and nitrogen 2020 M Grzechowiak, J Sliwiak, M Jaskolski- Frontiers in Plant, 2020 - ncbi.nlm.nih.gov vertebrate, and fungal GDHs have been deposited in the Protein Data Bank ( PDB ) In the present study, we report the crystal structure of AtGDH1 in apo form, as To provide background for functional and structural discussions, we investigated the evolutionary divergence of the
336 5vir 4ymi, 4fry Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target 2020 KH Burley, BJ Cuthbert, P Basu- ACS Infectious, 2020 - ACS Publications \ Interestingly, the three top-scoring NADP+ molecules are found in structures of Mtb nicotinamide-mononucleotide adenylyltransferase (NadD) (PDB ID: 4S1O) and Mycobacterium abscessus NadD (PDB ID: 4YMI and 5VIR). These results
337 5j3b - The translation elongation factor P in actinobacteria 2020 B Pinheiro Damasceno Florentino - 2020 - edoc.ub.uni-muenchen.de NC Nascent peptide-chain ORF Open reading frame PCR Polymerase chain reaction PDB Protein data EF- P facilitates translation of XPPX motifs is based in many structural studies... Structural superposition and ribbon representations of available EF-P structures. C. glutamicum (PDB code 6S8Z, orange, this work), Acinetobacter baumannii (PDB code: 5J3B, blue), E. coli (
338 5ts2 3pxu Phosphopantetheine Adenylyltransferase: A promising drug target to combat antibiotic resistance 2020 A Gupta, P Sharma, TP Singh, S Sharma- Biochimica et Biophysica Acta, 2020 - Elsevier Although, the DPCK domain of the human fusion protein shows high sequence and structural homology to bacterial DPCK The PDB IDs of the structure , percentage sequence identities and rms deviations for the C atoms are also indicated ... The structures of complexes of PPAT with dPCoA from several bacterial species have been determined so far and include EcPPAT (PDB ID: 1B6T), MtPPAT (PDB ID: 3RBA), BpPPAT (PDB ID: 3PXU), MaPPAT (PDB ID: 5O08), PaPPAT (PDB ID: 5TS2) and AbPPAT (PDB ID: 5ZZC
339 5vvw - Comparative modeling and dynamic simulation of UDP-N-acetylmuramoyl-alanine ligase (MurC) from Mycobacterium tuberculosis through virtual screening 2020 MA Isa- Life Sciences, 2020 - Elsevier The reference sequence (query sequence), searched against PDB and six proteins (1GQQ, 4HV4, 1P31, 2F00, 5VVW and 1J6U of its entire amino acids were in the most favorable region(Table 1). The G-factor of both the model of MurC, minimized model structure and the
340 4qtp - The SiaABC threonine phosphorylation pathway controls biofilm formation in response to carbon availability in Pseudomonas aeruginosa 2020 WH Poh, J Lin, B Colley, N Mller, BC Goh- BioRxiv, 2020 - biorxiv.org SiaC crystal 319 structure , and an anti-sigma factor antagonist from Mycobacterium paratuberculosis ( PDB ID: 320 4QTP ; gene ID MAP_0380; Fig 6D) was identified as the closest homologue (Z score of 9.0, an 321 amino-acid sequence
341 6bfu 6q04, 6tys, 6nb3, 6nb7, 6nb6 Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology-and bioinformatic-based predictions 2020 A Grifoni, J Sidney, Y Zhang- -HOST-MICROBE-D, 2020 - papers.ssrn.com with data about immune epitopes, protein structures , and host responses to virus infections (Pickett et al., 2012) glycoprotein structure ( PDB : 6ACD). The calculated surface of the top 10 amino acid residues Non- structural protein 3b 2 0 Protein 7a 2 0 Protein 9b 2 0
342 6vxx 6vyb Phytocompounds of Rheum emodi, Thymus serpyllum and Artemisia annua inhibit COVID-19 binding to ACE2 receptor: In silico approach 2020 R Rolta, D Salaria, V Kumar, A SOURIRAJAN, K DEV - 2020 - researchsquare.com proteins of COVID-19 were SARS-CoV-2 spike glycoprotein ( PDB ID: 6VXX ) and SARS-CoV-2 spike ectodomain structure ( PDB ID: 6VYB) and SARS coronavirus spike receptor-binding domain was Structural Bioinformatics Group, Berlin, Germany) for ADMET
343 5vwm - N-Hydroxyformamide LpxC inhibitors, their in vivo efficacy in a mouse Escherichia coli infection model, and their safety in a rat hemodynamic assay 2020 T Furuya, AB Shapiro, J Comita-Prevoir- Bioorganic & Medicinal, 2020 - Elsevier Fig. 2. Key interactions in the LpxC enzyme binding pocket observed in P. aeruginosa LpxCCHIR-090 (3) co-crystal structure ( PDB code: 5VWM ). We first implemented a docking model using the ICM-Pro software (Molsoft) based on the available co-crystal structures of P
344 4h3e - The Crystal Structure of the Manganese Superoxide Dismutase from Geobacillus stearothermophilus: Parker and Blake (1988) Revisited 2020 JJ Adams, CJ Morton, MW Parker- Australian Journal of Chemistry, 2020 - CSIRO determined primarily by X-ray crystallography, although one SOD structure has been SODs have also been determined from Pseudomonas putida (ovalis) ( PDB ID: 1dto acidocaldarius (1b06), [ 27 ] Acanthamoeba castellanii (6j55), [ 28 ] Trypanosoma cruzi ( 4h3e ), [ 29 ] Vigna
345 2mu0 2kok Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters 2020 MR Rosen, JB Leuthaeuser, CA Parish, JS Fetrow- Biochemistry, 2020 - ACS Publications Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs).... We performed MD simulations to better understand the conformational behavior of each of the nine classes of proteins identified by autoMISST. Starting structures for these simulations were obtained from the following data available in the RCSB PDB:34 group 3AAA, 2KOK (chain A); group 4AA, 2MU0 (chain A); gro
346 3mmt - The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis 2020 M Sharma, P Abayakoon, Y Jin, R Epa, JP Lingford - 2020 - chemrxiv.org Figure S15. Closed conformations of PfkB, TPK and SF kinases indicate close structural rela- tionship EcYihVADPMgSF structure reveals KRN sulfonate recognition triad in YihV A, FBPA from Bartonella henselae forms homotetramers ( 3MMT . pdb ),{, 2011 #8494} FBPA from
347 3ngj - Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1, 3-butanediol 2020 T Kim, PJ Stogios, AN Khusnutdinova, K Nemr- Journal of Biological, 2020 - ASBMB DERA structures as the best matches, including the Entamoeba histolytica DeoC ( PDB code 3NGJ ; Z score RMSD, 0.6 ; 66% sequence identity), and L. brevis DERA E78K mutant ( PDB code 4XBS; Z Based on the BH1352 structure , its active site is located inside of the -barrel
348 6c6b - Structural characterization, antifungal and cytotoxic profiles of quaternized heteropolysaccharide from Anadenanthera colubrina 2020 FOS Ribeiro, GS de Arajo, MGA Mendes- International Journal of, 2020 - Elsevier Volume 165, Part A, 15 December 2020, Pages 279-290. International Journal of Biological Macromolecules. Structural characterization, antifungal and cytotoxic profiles of quaternized heteropolysaccharide from Anadenanthera colubrina The 3D structures of all possible C. neoformans and M. canis targets were obtained from the Protein Data Bank (PDB) (Protein Data Bank, 2019) with the codes 2W3N (Carbonic anhydrase 2), 3Q73 (Farnesyl transferase), 5I33 (Adenylosuccinate synthetase), 5 U29 (Acetyl-coenzyme
349 4h3e - Parallel Molecular Evolution of Catalases and Superoxide DismutasesFocus on Thermophilic Fungal Genomes 2020 K Chovanov, M Bhmer, A Poljovka, J Budi- Antioxidants, 2020 - mdpi.com and heme catalases were obtained from Phyre-2 server [16] by employing the intensive mode with HMM and PSI-Blast for finding closest homologs with a known experimental structure . Obtained structural models were superimposed on experimental 3D structures using the
350 4f2n - Three Alkaloids from an Apocynaceae Species, Aspidosperma spruceanum as Antileishmaniasis Agents by In Silico Demo-case Studies 2020 D Morales-Jadn, J Blanco-Salas, T Ruiz-Tllez- Plants, 2020 - mdpi.com of this method can provide insights into the druggable targetome contained in the structural proteome criteria were chosen (vg to be a starting structure , to have a similar structure of a drawn using Marvin Sketch 19.15 converting the format of some structures into pdb files using ... Table A2. Enzymes crystal structures available in PDB server. 4f2n.1.A target SOD
351 6q09 - Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity 2020 Z Ma, ML Caldas Nogueira, DP Marchi-Salvador- ACS, 2020 - ACS Publications Journal Logo. Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity. Zhongxin Ma Zhongxin Ma. Burnett School of Biomedical
352 4ol9 4qji Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents 2020 HS Butman, TJ Kotz, CS Dowd- Frontiers in Cellular and, 2020 - ncbi.nlm.nih.gov This review gathers literature reports on the structure /mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway... To date, there is very little information available for the Mtb PanE homologue (MtPanE). The activity of the protein expressed by the putative panE gene (Rv2573) has not been experimentally verified, although its crystal structure bound to NADP+ and oxamate has been solved (PDB ID: 4OL9).
353 5t8s - MCSS-based Predictions of Binding Mode and Selectivity of Nucleotide Ligands 2020 R Gonzalez-Aleman, N Chevrollier, M Simoes- bioRxiv, 2020 - biorxiv.org method based on a coarse-grained model (RNA-LIM) was developed to model the structure of an on the protein-nucleotide complexes currently available in the Protein Data Bank (RCSB PDB (52 less than 2.0 and thus not representative of the currently available structural data
354 6uk3 3glq, 3n58, 3d64, 6aph, 5v96 S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains 2020 K Brzezinski- Biomolecules, 2020 - mdpi.com major [3G1U, unpublished], Cryptosporidium parvum [5HM8 unpublished], Acanthamoeba castellanii [ 6UK3 , unpublished], Naegleria Crystal structures of SAHases were acquired from PDB cofactor-binding domains was performed based on secondary structure assignments in
355 6nb4 6nb7 Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19) 2020 B Shanmugaraj, K Siriwattananon- Asian Pac J Allergy, 2020 - apjai-journal.org PDB ID 6CS2)72 and the following antibodies are shown in magenta: 80R ( PDB ID 2GHW)73, F26G1 ( PDB ID 3BGF)74, m396 ( PDB ID 2DD8)75, and S230 ( PDB ID 6NB7 (P D B ID 6NB4 ) Structure of SARS coronavirus spike receptor- binding domain complexed with receptor
356 4ni5 5jy1, 4weo Phylogenetics-based identification and characterization of a superior 2, 3-butanediol dehydrogenase for Zymomonas mobilis expression 2020 V Subramanian, VV Lunin- Biotechnology, 2020 - biotechnologyforbiofuels Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. ... The initial model was built based on PDB entry 4ni5 with FFAS03 search and ProtMod modeling servers [50,51,52] using the SCWRL method.
357 5v6d 4hr2, 4ek2, 6ay1, 4dut Structure, Folding and Stability of Nucleoside Diphosphate Kinases 2020 F Georgescauld, Y Song, A Dautant- International Journal of Molecular, 2020 - mdpi.com So far, 162 structures from 30 different species have been deposited within the Protein Data Bank ( PDB ) which fall to tetramer type II and two are isolated dimers [23,24,25] (Table 1). The structure of most tetramers was recently solved by a structural genomics approach yet ... 5v6d Neisseria gonorrhoeae in complex with citrate (1.85 Å) Abendroth, J.; Mayclin, S.J.; Lorimer, D.D.; Edwards, T.E.
358 4noz 4mh4 Substrate and product-assisted catalysis: molecular aspects behind structural switches along Organic Hydroperoxide Resistance Protein catalytic cycle 2020 R Mateus Domingos, RD Teixeira, A Zeida- ACS, 2020 - ACS Publications The Ohr active site architecture is composed of two cysteines structures (Figure S1). Notably, when analyzing the other Ohr structures available in the PDB , we observed that the position of the Arg-loop in the Bacillus subtilis OhrB (BsOhrB) structure presents an intermediate
359 3oc6 - BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization 2020 JE Snchez-Aparicio, L Tiessler-Sala - 2020 - chemrxiv.org Only 6- phosphogluconolactonase from mycobacterium smegmatis (which structure is accessible at the PDB with the code 3oc6 ) with an of BioMetAll in an artificial metalloenzyme framework, we started by looking for the His-His- Asp/Glu motif in the 6-PGLac structure
360 6mc0 - High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtiiAn Enzyme Involved in the Photosynthetic 2020 T Le Moigne, P Crozet, SD Lemaire, J Henri- International journal of, 2020 - mdpi.com 4A). Structural superposition of CrRPI1 with RpiA from Legionella pneumophila (LpRPI, PDB : 6MC0 , RMSD = 0.734 We describe the first structure of a ribose-5-phosphate isomerase from a Viridiplanta The structural fold of CrRPI1 (Figure 1B) is similar to previously described
361 5ez3 - Characterization of the Proteins Involved in the DNA Repair Mechanism in M. smegmatis 2020 A Di Somma, C Can, A Moretta, A Cirillo- International journal of, 2020 - mdpi.com The primary structure of the recombinant protein was verified by MALDI mapping strategy (Supplementary Materials, Table S4) and its correct folding assessed by circular The Acyl-CoA dehydrogenase from Brucella melitensis in complex with FAD ( PDB code 5EZ3 A) was
362 4dq8 - Green synthesis, antitubercular evaluation, and molecular docking studies of ethyl 3, 5-dicyano-6-oxo-2, 4-diarylpiperidine-3-carboxylate derivatives 2020 T Sekhar, P Thriveni, K Ramesh, PG Prasad- Medicinal Chemistry, 2020 - Springer Full size image. Fig. 4 figure4. a 3D structure view of molecular docking of compound 4c (green sticks) with Mycobacterium AckA protein (gray lines) The PDB file of the target protein downloaded from RCSB PDB (www.rcsb.org), AckA (PDBID: 4DQ8 )
363 6vxx - Bimodular effects of D614G mutation on the spike glycoprotein of SARS-CoV-2 enhance protein processing, membrane fusion, and viral infectivity 2020 X Jiang, Z Zhang, C Wang, H Ren, L Gao- Signal transduction and, 2020 - nature.com structure of S glycoprotein, we performed three-dimensional (3D) modeling with the template of published SARS-CoV-2 S structure ( 6vxx . pdb ) by the idea that the D614G mutation may affect the stability of the S protein trimer as suggested above based on structural analysis (Fig
364 5uxx - Diverse and unified mechanisms of transcription initiation in bacteria 2020 J Chen, H Boyaci, EA Campbell- Nature Reviews Microbiology, 2020 - nature.com Transcription of DNA is a fundamental process in all cellular organisms. The enzyme responsible for transcription, RNA polymerase, is conserved in general architecture and catalytic function across the three domains of life. ... Fig 5 Mycobacterium tuberculosis σK–RskA (PDB ID 4NQW; panel Ae) 85, Bartonella quintana σE–NepR (PDB ID 5UXX: panel Af),
365 6ao8 - Mutations in ArgS Arginine-tRNA Synthetase Confer Additional Antibiotic Tolerance Protection to Extended-Spectrum--Lactamase-Producing Burkholderia 2020 H Yi, J Park, KH Cho, HS Kim- Antimicrobial Agents and, 2020 - Am Soc Microbiol To investigate the ArgS function affected by the mutations, we first computationally predicted the B. thailandensis ArgS structure by using the homologous structure of Neisseria gonorrhoeae (PDB accession no. 6AO8) using Modeller
366 6q06 - Molecular diversity of coronavirus host cell entry receptors 2020 JK Millet, JA Jaimes, GR Whittaker- FEMS microbiology reviews, 2020 - academic.oup.com boxes indicate genes encoding accessory proteins (ns2, ns4a, ns4b and ns5a), while green boxes indicate structural proteins B) Representative structure of coronavirus protein in pre-fusion (S1 and S2 subunits, PDB 3JCL) and post-fusion (S2 subunit, PDB 6B3O) conformations ...MERS-CoV NTD (PDB 6Q06), which binds sialosides with a preference for α2,3-linked sialic acids,
367 6c49 - In silico study of the structure and ligand interactions of alcohol dehydrogenase from cyanobacterium Synechocystis Sp. PCC 6803 as a key enzyme for biofuel 2020 O Haghighi, M Moradi- Applied Biochemistry and Biotechnology, 2020 - Springer with amino acids in Zn ion binding sites along with a slight deviation between Cys 110 in the template and Cys 106 in the homology model in the location of structural Zn PCC 6803 homology model (Cyan) superimposed onto the template crystal structure ( PDB ID: 6C49 ) (Tan
368 4f47 - Post-translational Succinylation of Mycobacterium tuberculosis Enoyl-CoA Hydratase EchA19 Slows Catalytic Hydration of Cholesterol Catabolite 3-Oxo-chol-4,22 2020 AC Bonds, T Yuan, JM Werman, J Jang- ACS Infectious, 2020 - ACS Publications Cholesterol is a major carbon source for Mycobacterium tuberculosis (Mtb) during infection, and cholesterol utilization plays a significant role in persistence and virulence within host macrophages...
369 6ok4 - Chlamydia trachomatis glyceraldehyde 3phosphate dehydrogenase: Enzyme kinetics, highresolution crystal structure, and plasminogen binding 2020 N Schormann, J Campos, R Motamed- Protein, 2020 - Wiley Online Library Chlamydia trachomatis glyceraldehyde 3phosphate dehydrogenase: Enzyme kinetics, highresolution crystal structure , and plasminogen binding. Norbert Schormann We describe here the highresolution crystal structure of the holo enzyme refined at 1.5 resolution
370 6vxx - Structural impact of mutation D614G in SARS-CoV-2 spike protein: enhanced infectivity and therapeutic opportunity 2020 A Fernndez- ACS medicinal chemistry letters, 2020 - ACS Publications Figure 1. Structural and epistructural interactions at the S1/S2 interface in the spike protein of SARS-CoV-2. (a) Positioning of D614 in the S1 chain (magenta) relative to T859 in the S2 chain (blue) at the S1/S2 interface for the spike protein structure reported in PDB6VXX
371 3t7c 3s55 Structural studies on M. tuberculosis decaprenyl phosphoryl--D-ribose epimerase-2 enzyme involved in cell wall biogenesis 2020 SP Gangwar, A Bandyopadhyay, AK Saxena- bioRxiv, 2020 - biorxiv.org The MtbDprE2 structure was aligned with structures of PDB database using TM- structural alignment program of I-TASSER server, which yielded ten closest structural homologs (as coverage=97.2% [54] (vi) PDB - 3t7c , identity=13.3%, coverage=97.2% [55] (vii) PDB -1ipe
372 3tv2 3gtd, 3qbp, 3rd8 Structural, biochemical and biophysical characterization of recombinant human fumarate hydratase 2019 MA Ajalla Aleixo, VL Rangel, JK Rustiguel- The FEBS, 2019 - Wiley Online Library code: 3GTD; [37]), Burkholderia pseudomallei FH (BpFH, PDB code: 3TV2 ; results not (MsFH, PDB code: 3RD8; [38]). The superposition of C atoms between HsFH and the From the structure -based drug design perspective, it is imperative to identify
373 3v7o - Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription 2019 A Ivanov, P Ramanathan, C Parry, PA Ilinykh- Cellular and Molecular, 2019 - Springer Three-dimensional structural models were built for NP, VP35, VP40, GP, VP30 and VP24 proteins using available crystal structures or by de novo structure prediction to elucidate the potential role of the phosphorylation sites
374 5b8i - Biochemical, Biophysical, and Functional Analyses of Two Isoforms of the SnRK2 inhibitor AtSCS 2019 K Tarnowski, M Klimecka, A Ciesielski, G Goch, A Kulik- bioRxiv, 2019 - biorxiv.org 5a, 02-106 Warsaw, Poland 20 2 Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland 21 3 The Norwegian Center for Structure Biology, Institute of Chemistry, University of 22 Functional and structural studies showed that PP2Cs 110
375 3laa 3la9 Recent advances in the understanding of trimeric autotransporter adhesins 2019 AR Kiessling, A Malik, A Goldman- Medical Microbiology and Immunology, 2019 - Springer ring (Orange) domains. c Top view of Hia BD1( PDB ID:1S7M) rep- resenting tryptophan side chain from each monomer. d Structure of BpaA ( PDB ID: 3LAA ) representing FGG (Violet purple), short neck (Olive), head (Teal), long neck (Blue) domains
376 4xgi - Homology Modeling and Molecular Docking Studies of Glutamate Dehydrogenase (GDH) from Cyanobacterium Synechocystis sp. PCC 6803 2019 O Haghighi, S Davaeifar, HS Zahiri, H Maleki- International Journal of, 2019 - Springer aLigand name in structure : NAD-507 Docking pose number Reference ligand in crystallography structure (ligand name and pdb code) NADH NADPH AKG Glutamate 1V9L 1HWYa 5GUD 5IJZ 1HWY 4XGI 6DHM 3AOG Pose 01 4.57 3.48 5.74 5.75 2.22 2.11 1.72 1.58
377 5deo - Novel antimycobacterial compounds suppress NAD biogenesis by targeting a unique pocket of NaMN adenylyltransferase 2019 AL Osterman, I Rodionova, X Li, E Sergienko- ACS chemical, 2019 - ACS Publications ADVERTISEMENT. Log In Register. Cart. ACS; ACS Publications; C&EN; CAS. ACS Publications: ACS Journals; ACS eBooks; C&EN Global Enterprise. A; Accounts of Chemical Research; ACS Applied Bio Materials; ACS Applied Electronic
378 4lfy - Pyrimidine biosynthesis in pathogensStructures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae 2019 J Lipowska, CD Miks, K Kwon, L Shuvalova- International journal of, 2019 - Elsevier As the first DHO structure ( PDB ID 1J79) was deposited in 2001, structural information was not available to guide the DHO classification proposed in 1999. In 2014, an updated phylogenetic tree based on structure -guided sequence alignments using structures available for nine .. Table 1 Burkholderia cenocepacia 4LFY 2013 Structural genomics (SSGCID)
379 4j3g - PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS 2019 B Strauss - 2019 - scholarworks.sjsu.edu set. Validated residue binary assignments of 0 (no change in secondary structure ) and 1 (change in secondary structure ) were determined (DSSP) from 3D X-ray structures for sets of virtually identical chains crystallized under different conditions
380 4fkx - Characterization of crystal structure and key residues of Aspergillus fumigatus nucleoside diphosphate kinase 2019 Y Hu, X Jia, Z Lu, L Han- Biochemical and biophysical research, 2019 - Elsevier was determined by molecular replacement (MR) method using Trypanosoma brucei NDK (TbNDK, PDB code 4FKX ) as starting The PDB accession code was 6AGY 1230-1247. Google Scholar. [9] L. Moynie, MF Giraud, F. Georgescauld, I. Lascu, A. DautantThe structure of the
381 5i0p - STRUCTURE AND FUNCTION OF THE PALMITOYLTRANSFERASE DHHC20 AND THE ACYL COA HYDROLASE MBLAC2 2019 MIP Malgapo - 2019 - ecommons.cornell.edu crystals ..... 43 The overall structure of hDHHC20 and zfDHHC15 is similar to what was predicted for DHHC enzymes .... 44 Two zinc ions serve a structural function in the cysteine-rich domain of DHHC20 ..... 44
382 3enk - Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum 2019 YW Nam, M Nishimoto, T Arakawa, M Kitaoka- Scientific reports, 2019 - nature.com Here, we focused on structural features of GalE from B. longum JCM1217 (bGalE) The main chain structure of bGalE is similar to those of bacterial and eukaryotic GalEs. C RMSD values (distance cutoff = 2.0 ) of the UDP-GlcNAc complex with hGalE ( PDB ID 1HZJ, ... We built a reliable homology model of BLLJ_1592 (GQME = 0.72 and QMEAN = −2.34) using the SWISS-MODEL server45 with an unpublished structure of GalE from Burkholderia pseudomallei (PDB ID: 3ENK, sequence identity = 42.3%) as a template
383 3qxz - Crystal Structure of a Novel Type Isomerase of Enoyl-CoA Hydratase/Isomerase Family Protein from Cupriavidus necator H16 2019 H Seo, KJ Kim- Biotechnology and Bioprocess Engineering, 2019 - Springer code 5Z7R, Z-score 31.5 and 1.7 rmsd) and probable enoyl- CoA hydratase/isomerase from Mycobacterium abscessus ( PDB code 3QXZ , Z-score has highly conserved enoyl-CoA hydratase fold but its functional implication cannot be obtained from the overall structure
384 4hwg - Energy Landscape of the Domain Movement in Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase 2019 C de Azevedo, AS Nascimento- bioRxiv, 2019 - biorxiv.org chain without ligands PDB ID Organism Ligands Oligomeric state CV Angle Chain A (deg) Rickettsia bellii ( 4HWG ). We hypothesize that the cubic symmetry observed in this crystal (UDP-GlcNac) and cofactor (UDP) are found bound in the crystal structure (1VGV, 3BEO, 4FKZ
385 4iwh - Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data 2019 JT Seffernick, SR Harvey, VH Wysocki- ACS Central, 2019 - ACS Publications from which data have been favorably compared to known crystal structures on many along with other bioanalytical MS and dissociation techniques, yields useful structural information, the sparse, not allowing for an unambiguous determination of the protein complex structure... Additionally, the Pnear also improved for 56/57 ideal cases (except 4IWH) when SID data were used, as shown in Figure S3A.
386 3i3r - Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates 2019 JA Ribeiro, SM Chavez-Pacheco- Section D: Structural, 2019 - scripts.iucr.org mode and protein conformation, we solved the structure of the MtDHFRNADPHDIA ternary complex and compared it with the structure of the of MtDHFRNADPHPMX (yellow) and the B. bovis DHFR domain in complex with NADPH and PMX ( PDB entry 3i3r ; Begley et
387 3hzu 3hwi Mycobacterium tuberculosis CysA2 is a dual sulfurtransferase with activity against thiosulfate and 3-mercaptopyruvate and interacts with mammalian cells 2019 AN Meza, CCN Cambui, ACR Moreno, MR Fessel- Scientific reports, 2019 - nature.com dimensional structures of M. tuberculosis CysA2 ( PDB code 3HIW, yellow), CysA3 ( PDB code 3AAY, red) and SseA ( PDB code 3HZU , blue) Based on the available three-dimensional structure of CysA2, we performed a comparison with putative orthologues studied in the
388 5cy4 - Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence 2019 L Calvanese, F Squeglia, M Romano- Structure and, 2019 - Taylor & Francis Despite this, its structure , a dimeric molecule with each monomer adopting a compact entry 4OKE) from Mycobacterium tuberculosis against the Protein Data Bank ( PDB ) using the Coxiella burnetii (Coxbu) (3TR8, Z-score 13.8), Acinetobacter baumannii (Aciba) ( 5CY4 , Z-score
389 2klx 3fq3, 3hhj Potential druggable proteins and chimeric vaccine construct prioritization against Brucella melitensis from species core genome data 2019 M Aslam, M Shehroz, M Shah, MA Khan, SG Afridi- Genomics, 2019 - Elsevier The radius of gyration was also predicted to assess the compactness of structure and the Gene symbols, PDB homolog ID's, Protein Names, Model C-score, Template Vs model RMSD BME_RS00875, 2KLX , glutaredoxin 3, 0.89, 2.0 1.6 , 98.718, 2.88, 0.99 (26), 9419.75, 3.27
390 5dvw - Computational Drug Design against Ebola Virus Targeting Viral Matrix Protein VP30 2019 A Venkatesan, L Ravichandran- Borneo Journal of, 2019 - journal.umpalangkaraya.ac.id Protein structure preparation The protein crystal structure of Ebola VP30 protein ( PDB code: 5DVW ) with the resolution of 1.75 was retrieved from RCSB Protein Data Bank ( PDB ), a repository providing crystal structures of biotic macromolecules (Berman et al., 2000)
391 3laa - Structure of the UspA1 protein fragment from Moraxella catarrhalis responsible for C3d binding 2019 KM Mikula, R Kolodziejczyk, A Goldman- Journal of structural biology, 2019 - Elsevier 2012) as found in SadA (2YO2, 2YNZ) (Hartmann et al., 2012) or BpaA ( 3LAA ) (Edwards et CCP4 package (Winn et al., 2011) with the structure of UspA1 165366 ( PDB : 3PR7) (Agnew Model of UspA1 299452 structure solved in this study, neck and coiled-coil domains; chain
392 5cy4 - Characterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular disulfide bond for homodimer formation and nuclease activity 2019 Y Piotrowski, K Berg, DP Klebl, I Leiros- FEBS open, 2019 - Wiley Online Library campestris, PDB 1J9A: Haemophilus influenzae, PDB 2IGI: E. coli, PDB 3TR8: Coxiella burnetii, PDB 5CY4 : Acinetobacter baumannii) In the X. campestris Orn structure ( PDB 2GBZ) it is shown that Orn forms a dimer in the crystal From the structural analysis it was shown that
393 3i4e 3oq8, 3e5b, 3p0x, 3eol Mechanistic Insights into the Catalytic Mechanism and Inhibition of Mycobacterium Tuberculosis Isocitrate Lyase 2019 S Ray - 2019 - ubir.buffalo.edu an attractive target for drug development. 1.4.3 Structure of ICL Aspergillus nidulans [ PDB ID: 1DQU],67 M. tuberculosis [ PDB ID: 1F61, 1F8I, 1F8M, 5DQL],68- 69 Escherichia coli [ PDB ID:1IGW]70, Burkholderia pseudomallei [ PDB ID: 3I4E (paper
394 4xfd - Validation of NAD synthase inhibitors for inhibiting the cell viability of Leishmania donovani: In silico and in vitro approach 2019 H Mandal, S Vijayakumar, S Yadav- Structure and, 2019 - Taylor & Francis Skip to Main Content
395 3nf4 - Crystal Structures of Putative Flavin Dependent Monooxygenase from Alicyclobacillus Acidocaldarius 2019 H Moon, S Shin, J Choe- Crystals, 2019 - mdpi.com was obtained using the Molrep program of CCP4 package [13] with Acyl-CoA dehydrogenase (M. thermoresistibile) structure ( PDB ID: 3NF4 ) as a The data collection and refinement statistics are summarized in Table 1. The coordinate and structure factors for apo and FAD
396 4qhq - Structural insights into the substrate specificity of SP_0149, the substrate-binding protein of a methionine ABC transporter from Streptococcus pneumoniae 2019 B Jha, R Vyas, J Bhushan, D Sehgal- Section F: Structural, 2019 - scripts.iucr.org Z-score Rmsd (A ) Nalign %seq} Bound substrate PDB code Protein name and description 15.2 1.36 223 41 Met 4qhq A nutrient-binding protein (bound to methionine in the Sequence identity in SSM is calculated from structure (three-dimensional), rather than sequence
397 3oc6 3v2i, 3ico Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application 2019 C Oh, TD Kim, KK Kim- Crystals, 2019 - mdpi.com In the Protein Data Bank ( PDB ), 136 crystal structures of bacterial CEHs (424 PDB codes) from The // sandwich architecture is most frequently found in CEHs, but 3-solenoid, are widely used in industrial applications, and are the objects of research in structure - or mutation ... 6-phosphogluconolactonases from M. smegmatis (representative PDB code: 3OC6) [140] belonging to group 3-4 CEHs contains His151-Glu149 as a catalytic dyad with nucleophilic water (Figure 3I).
398 3k5p - 3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis 2019 N Paczia, J Becker-Kettern, JF Conrotte- Biochemistry, 2019 - ACS Publications Structural Biology Unit, CIC bioGUNE Technological Park of Bizkaia, 48160 Derio , Vizcaya , Spain. IKERBASQUE, Basque Foundation for Here, we provide a detailed biochemical and sequence structure relationship characterization of the yeast PHGDH homologues
399 6d6j 3oj7 Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc (II)-Binding Residues in Sites with Four Protein Ligands 2019 M Macchiagodena, M Pagliai, C Andreini- Journal of chemical, 2019 - ACS Publications quantum mechanical calculations on a training set of high-quality protein structures , encompassing the in the catalytic reaction of enzymes, by stabilizing the tertiary/quaternary structure of a cells.(5,7) The high thermodynamic stability of the tetrahedral zinc(II) structural sites in
400 3ido - The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis 2019 SB Pereira, M Santos, JP Leite, C Flores- , 2019 - Wiley Online Library We clarified the roles of both proteins through biochemical and structural analysis, pro viding the first A threedimensional protein structure alignment was performed using representative LMWPTP sequences from the eukaryote E. histolytica ( PDB : 3ido ; UniProt:C4LSE7
401 4egq 4egj, 4eg0 Burkholderiapseudomallei dalaninedalanine ligase; detailed characterisation and assessment of a potential antibiotic drug target 2019 L DazSez, LS Torrie, SP McElroy, D Gray- The FEBS, 2019 - Wiley Online Library An apo-BpDdl structure ( PDB code 4EGQ ) has been determined by the Seattle Structural Genomics Center for Infectious Disease. Electron and difference density maps in the ATP binding sites were inspected to ascertain if a ligand might be present
402 4gie - Trypanocidal Mechanism of Action and in silico Studies of p-Coumaric Acid Derivatives 2019 SP Lopes, YP Castillo, ML Monteiro- International journal of, 2019 - mdpi.com In this work, twelve compounds were prepared, maintaining the (E)-3-(4-hydroxyphenyl) acrylic acid structure and modifying only the radical R for 7, C-8, C-9), being six from the aromatic ring and three from the side chain with the presence of carbonyl that confirms the structures
403 3rr2 3hwi Caracterizao da via de captura/assimilao de sulfato em Mycobacterium tuberculosis: estratgias para o desenvolvimento de inibidores e potenciais alvos para 2019 AN Cerone - 2019 - repositorio.unicamp.br transport of several substances essential to the survival of organisms, which are poorly characterized in M. tuberculosis, the elucidation of structures and molecular SubI was expressed and purified and had its three-dimensional structure solved in the
404 5jy1 - Clean Enzymatic Oxidation of 12Hydroxysteroids to 12OxoDerivatives Catalyzed by Hydroxysteroid Dehydrogenase 2019 F Tonin, N Alvarenga, JZ Ye- Advanced Synthesis, 2019 - Wiley Online Library MODEL (https://swissmodel.expasy.org/ interactive), employing the crystal structure of the putative SDR from Burkholderia xenovorans ( PDB ID: 5JY1 .1) as determination of the cosubstrate specificity of these enzymes.[11] The 3D model of the El12-HSDH structure showed a
405 3f9i - Identifying Novel Inhibitors of RpFabG in Typhus-inducing Rickettsia prowazekii 2019 A Panatpur - 2019 - repositories.lib.utexas.edu The Virtual Cures stream streamlines the aforementioned process by virtually analyzing the structural and chemical bonding relationships a 3-dimensional crystal structure is present for 3-ketoacyl-(acyl-carrier-protein) reductase [ PDB 3F9I ], the available structure has not
406 4ffc - Crystal structure of -aminobutyrate aminotransferase in complex with a PLP-GABA adduct from Corynebacterium glutamicum 2019 J Hong, KJ Kim- Biochemical and biophysical research communications, 2019 - Elsevier microorganisms, including P. aurescens (PaGABA-AT, PDB code 4ATP), Mycobacterium abscessus (MaGABA-AT, PDB code 4FFC ), and E. coli (EcGABA-AT, PDB code 1SF2) (Fig of CgGABA-AT with that of other GABA-ATs, we superimposed the CgGABA-AT structure and all
407 3ixc - Activity Assessment of a Halophilic -carbonic Anhydrase from the Red Sea Brine Pool Discovery Deep 2019 A Vancea - 2019 - repository.kaust.edu.sa 25 CA_D 3R1W 3TIO 2FKO 3R3R 3IXC 3VNP 1XHD 4N27 1QRG 3KWC Figure 7: Structural homology study - structural overlay of CA_D monomer with reported PDB structures Table 2: List of the PDB structure used in the structure homology study together with the organism
408 3pk0 5if3 Two enantiocomplementary Ephedrine Dehydrogenases from Arthrobacter sp. TS-15 with broad substrate specificity 2019 T Shanati, C Lockie, L Beloti, G Grogan- ACS, 2019 - ACS Publications provide a detailed insight into both the functional and structural characteristics of PseDH and EDH.. A comparison with 30 structures of SDRs from bacterial species in the PDB suggests that S143 is most commonly a small hydrophobic residue, such as G, A, or V, whereas W152 is most commonly an H, M, or L, although in SDRs from Burkholderia vietnamiensis (5IF3) and Mycobacterium smegmatis (3PK0) the residue is W
409 5unb - Janus kinase inhibition for autoinflammation in DNASE2 deficiency 2019 S Nanthapisal, A Cavounidis, H Takeshita- Journal of Allergy and, 2019 - ora.ox.ac.uk Structural modeling Structural models and figures were prepared by using the ICM software package (MolSoft, San Diego, Calif). A homology model for human DNase II was prepared by using the existing structure from B thailandensis ( PDB 5UNB ) as the model template
410 3tmg - Examination of the Glycine Betaine-Dependent Methylotrophic Methanogenesis Pathway: Insights Into Anaerobic Quaternary Amine Methylotrophy 2019 AJ Creighbaum, T Ticak, S Shinde, X Wang- Frontiers in, 2019 - frontiersin.org We therefore generated models of MV8460 using the apo-crystal structure of DhMtgB ( PDB 2QNE) as a (A) The models represent the aligned global structure of DhMtgB Various crystal structures of GB-binding enzymes; 1R9L (Schiefner et al., 2004), 6EYG, 3TMG (Li et al
411 5elo 6aqg, 5vl1, 6c86 Side chain rotameric changes and backbone dynamics enable specific cladosporin binding in Plasmodium falciparum lysyltRNA synthetase 2019 J ChhibberGoel, A Sharma- Proteins: Structure, Function, and, 2019 - Wiley Online Library ( PDB : apo 6C86, holo 5ELO ) and M. ulcerans (MuKRS) ( PDB : apo 5VL1, holo re-arrangements and are noted as 1 to 4 for all the four PDB data sets (Table 1 and Fig. 1). In based on structural analyses. Our analyses also provide a platform for structure -guided
412 5vwm - Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria 2019 JP Surivet, P Panchaud, JL Specklin- Journal of Medicinal, 2019 - ACS Publications UDP-3-O-((R)-3-hydroxymyristoyl)-N-glucosamine deacetylase (LpxC) is as an attractive target for the discovery and development of novel antibacterial drugs to address the critical medical need crea...
413 3s99 - Identification and characterization of ABC transporters for carbohydrate uptake in Thermus thermophilus HB8 2019 M Chandravanshi, A Sharma, PD Gupta, SK Mandal- Gene, 2019 - Elsevier substantiate the relationship of TTHV089 with XBPs, its three-dimensional tertiary structure was predicted All the programs utilized XBP from E. coli (EcXBP, PDB id: 3M9W, open Further, the structural homology search using the predicted model of TTHV089 shows that apart
414 3pfd - Site-directed mutation to improve the enzymatic activity of 5-carboxy-2-pentenoyl-CoA reductase for enhancing adipic acid biosynthesis 2019 J Yang, Y Lu, Y Zhao, Z Bai, Z Ma, Y Deng- Enzyme and Microbial, 2019 - Elsevier 3PFD was the PDB ID of the template. Therefore, we used 3PFD as the template to build the homology model of Tfu_1647 protein using DS 2017R2 [17] We then used the Deriding-like force field in DS 2017R2 to optimize the structure to ensure that we produced a
415 3sbx - (p) ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch 2019 YE Zhang, RL Brentsen, T Fuhrer, U Sauer, K Gerdes- Molecular cell, 2019 - Elsevier marinum showing similarity to the PpnN core domain and determined in the presence of adenosine monophosphate (AMP) ( PDB : 3SBX , Figure S3 Vibrio cholerae and Idomarina baltica, at a similar position to the phosphate of AMP in the M. marinum structure , suggesting that
416 4ol9 - Genome-wide survey and crystallographic analysis suggests a role for both horizontal gene transfer and duplication in pantothenate biosynthesis pathways 2019 B Khanppnavar, R Chatterjee, GB Choudhury- et Biophysica Acta (BBA, 2019 - Elsevier helix in the N-terminal domain (H2, residues 3341) which is typically absent in other well-characterized KPRs such as Escherichia coli (1KS9), S. aureus (4YCA), and M. tuberculosis ( 4OL9 ) (C) Cartoon representation of crystal structure of PaKPR in PDB accession, 5ZIK, 5ZIX
417 4g7f - HUMANIDADES, CIENCIA, TECNOLOGA E INNOVACIN EN PUEBLA 2019 CAS BALTAZAR, UNMM INMUNIZADO, C ORAL - academiajournals.com Page 1. HUMANIDADES, CIENCIA, TECNOLOGA E INNOVACIN EN PUEBLA ISSN 2644-0903 online VOL. 2, NO. 1, 2020 WWW.ACADEMIAJOURNALS.COM TRABAJO DE INVESTIGACIN AUSPICIADO POR EL CONVENIO CONCYTEP-ACADEMIA JOURNALS
418 6c9c - Disorder and interfaces in proteins are two sides of the same coin 2019 B Seoane, A Carbone- bioRxiv, 2019 - biorxiv.org c. Analysis of cluster 6c9c A ( PDB IDs for the structures are given in SI section S2). In the external wheel, we show one unbound structure and the chain structures containing the 12 different interfaces of this cluster: DRs in orange and IRs in blue
419 3mx6 - Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity 2019 SC Bala, N Haque, V Pillalamarri, R Reddi- International journal of, 2019 - Elsevier 3MX6 , R. prowazekii, 99% (C), 1% (L) Based on this analysis, MetAP1n has different active site architecture and hence has a substrate preference for leucine in addition 3c. Column 2 describes the result analysis of the HSSP file associated with EcMetAP1a structure ( PDB : 1C21
420 5td3 - Cloning, expression and characterization of catechol 1, 2-dioxygenase from Burkholderia cepacia 2019 TVN Thi, DDH Sinh, THT Le, ND Huy- The Journal of general, 2019 - jstage.jst.go.jp Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: 337 quantitative structure /activity relationship and the crystal structures of native enzyme 338 radioresistens LMG S13 ( PDB : 2XSU), B. vietnamiensis LMG 22486 ( PDB : 5TD3 ), R. 375
421 5vcu - In-silico study of flavonoids from Cassia tora as potential anti-psoriatic agent 2019 I Akachukwu, EE Amara- Journal of Applied Pharmaceutical, 2019 - japsonline.com 4; CCS ( PDB 5QC5) cathepsin S; JAK-3 ( PDB 5TTS) Janus kinase; RAC-1 ( PDB 5VCU ) Ras-related a vital structural requirement for strong binding with the target proteins The validity of the suggested structure - activity relationship is predicated on the observed reduction of
422 3s99 - The evolving story of AtzT, a periplasmic binding protein 2019 ML Dennis, L Esquirol, T Nebl, J Newman- Section D: Structural, 2019 - scripts.iucr.org (2019). D75, 9951002 Page 5. cluster protein and had electron density in the binding site for a purine. Post hoc analysis of the structure and sequence showed that PDB entry 3s99 has 54% sequence identity and an rmsd of 1.2A (over $330 residues) to AtzT
423 3swt - Non-Heme Iron Oxygenases: An Investigation of the Protein Ligand Effects on the Chemical Reactivity in MiaE and Cysteamine Dioxygenases 2019 P Palacios - 2019 - rc.library.uta.edu enzyme toluene monooxygenase in Figure 1.1 (panel B).14 The structural frame of the non-heme iron Figure 1.2 X-ray crystal structure of the Fe(II)/-ketoglutarate dependent enzyme TauD from Myobacterium marinum ( PDB : 3SWT )22 Page 22. 10
424 4pfz - Structural insights into a maleylpyruvate hydrolase from sphingobium sp. SYK-6, a bacterium degrading lignin-derived aryls 2019 H Hong, H Seo, KJ Kim- Biochemical and biophysical research, 2019 - Elsevier delta-isomerase from Mycobacterium smegmatis strain ATCC 700084 ( PDB code 4PFZ , 41% sequence The model building and structure refinement were performed as in SsMPH Apo type Mn 2+ -pyruvate have been deposited in the Protein Data Bank with PDB codes 6JVV
425 5u25 - FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function 2019 L Trisolini, N Gambacorta, R Gorgoglione- Journal of Clinical, 2019 - mdpi.com Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure , although the investigated Similarly, AIF-crystallized structure hosts a FAD and two NADH molecules (4bur. pdb , [26]) and
426 5w25 - Impact of Target-Based Drug Design in Anti-bacterial Drug Discovery for the Treatment of Tuberculosis 2019 AC Pushkaran, R Biswas, CG Mohan- Structural Bioinformatics, 2019 - Springer Table 3 Crystal structure of the key druggable targets in Mtb. Molecular target. Pathways involved. PDB ID. DprE1. Arabinogalactan biosynthesis AspS. Protein synthesis. 5W25 . Peptide Deformylase. Maturation of nascent polypeptides. 3E3U. DNA Gyrase
427 5vwm - In silico study of various compounds from essential oil of Cymbopogon winterianus against Pseudomonas aeruginosa targets 2019 Moura, A Monteiro, M Maia, N Sousa, G Rodrigues - 2019 - pdfs.semanticscholar.org Protein resolution values were 2.1 for ExoA ( PDB ID 1XK9), 1.8 for LpxC ( PDB ID 5VWM ) and 2.31 for PBP3 ( PDB ID 4KQO). All presented inhibitors coupled to their crystallographic structure , which allowed the delimitation of the active site of each protein
428 4qtp - SiaABCDA threonine phosphorylation pathway that controls biofilm formation in Pseudomonas aeruginosa 2019 WH Poh, J Lin, B Colley, N Mller, BC Goh- BioRxiv, 2019 - biorxiv.org 7NTU Institute of Structural Biology, Nanyang Technological University, Singapore 18 Biofilms are ubiquitous, multicellular structures embedded in a self-made matrix, that can suspended biofilms greatly influence the development, structure and function of their surface-attached
429 5b8h - Identification of Specific and Nonspecific Inhibitors of Bacillus anthracis TypeIII Pantothenate Kinase (PanK) 2019 JA Shapiro, JJ Varga, D Parsonage, W Walton- , 2019 - Wiley Online Library Organic synthesis of analogues along with biochemical validation of the proposed mechanism will allow structure function analysis and form 2H3G, DOI: 10.2210/pdb2H3G/ pdb ), PaPanK ( PDB ID: 2F9T, DOI: 10.2210/pdb2F9T/ pdb ), and BcPanK ( PDB ID: 5B8H , DOI: 10.2210
430 5j92 - Preferential catabolism of the (S)enantiomer of the herbicide napropamide mediated by the enantioselective amidohydrolase SnaH and the dioxygenase Snpd in 2019 J Huang, D Chen, J Jiang- Environmental microbiology, 2019 - Wiley Online Library molecular docking. A homology model of Snpd was built based on chain A of the 5J92 template (sharing 39% identity with Snpd; PDB code; resolution: 1.95 ). A Snpd- KG-FeO complex structure was established in a similar manner as SnaH-Zn-H2O. The
431 3ido 3jvi Vibrio cholerae LMWPTP-2 display unique surface charge and grooves around the active site: Indicative of distinctive substrate specificity and scope to design specific 2019 S Chatterjee, S Nath, B Ghosh, U Sen- Biochimica et Biophysica Acta (BBA, 2019 - Elsevier The surface properties of VcLMWTP-1, although have some distinct features, resembles closely to that of E. histolytica LMWPTP ( PDB : 3IDO ) This closure at the P-loop is also evident from the structural alignment with an 'open structure ' of apo-MPtpA ( PDB : 2LUO) [41] to the
432 4ix8 - Biochemical and structural characterization of tyrosine aminotransferase suggests broad substrate specificity and a two state folding mechanism in Leishmania 2019 S Sasidharan, P Saudagar- FEBS Open Bio, 2019 - Wiley Online Library outlier region. PROSA score of PM0081305 was -8.56 and the score remained in the region of known native structures . The template structure that was taken for modeling ( PDB ID: 4IX8 ) had a PROSA score of -8.89. The structure
433 3u5w - The crystal structure of Rv2991 from Mycobacterium tuberculosis: An F420 binding protein with unknown function 2019 S Benini, A Haouz, F Proux, P Alzari- Journal of structural biology, 2019 - Elsevier from M. tuberculosis in complex with F 420 (Ahmed et al., 2016); 3U5W uncharacterized protein of secondary structural elements of the query (Rv2991) that match the target structure by the sequence similarity search by BLASTp when Rv2991was compared to the whole PDB
434 3uam - Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region 2019 R Arora, P Bharval, S Sarswati, TZ Sen- Journal of Molecular, 2019 - Elsevier pdb ) id: 2vtc, 2yet, 3zud, 4b5q, 4eir, 4qi8, 5acf, 5aci, 5acj, 5foh, 5tkf, 5tkg, 5tkh, and 5tki) and 10 structures in AA10 ( pdb id: 2bem, 3uam , 4ow5, 4oy6 MSF correlation value of 0.58 or higher (Table 1). In the case of AA11 and AA13 there was only one structure , 4mah and 5t7j
435 5vmk 4eqy Mechanistic characterisation and inhibitor identification of Mycobacterium tuberculosis bifunctional N-acetyltransferase/uridylyltransferase GlmU 2019 PD Craggs - 2019 - discovery.ucl.ac.uk that has contributed to the success of this pathogenic over the last thousand years. Peptidoglycan is a unique and essential structural element that provides much of the Structure of UDP-GlcN Table 7. Published GlmU structures in the Protein Data Bank ( pdb ) ....70
436 4wbs - The structure of lipopolysaccharide transport protein B (LptB) from Burkholderia pseudomallei 2019 G Pankov, A Dawson, WN Hunter- Section F: Structural Biology, 2019 - scripts.iucr.org A single polypeptide from Paraburkholderia phymatum LptB ( PDB entry 4wbs ; Seattle Structural Genomics Center 2. The LptB subunit fold is conserved and displays no major conformational differences irrespective of whether the cofactor is present in the structure or not
437 3uam - Chitin-Active Lytic Polysaccharide Monooxygenases 2019 G Courtade, FL Aachmann- Targeting Chitin-containing Organisms, 2019 - Springer 3UAM . Likely active on chitin. To be published The structures were made using PyMol and the PDB code 2BEM. The copper coordinates were extracted from the PDB code 2YOX The structure is stabilized by hydrophobic residues, as well as by one or two disulfide bridges CANNOT DECIDE, RIGHT TARGET AND FIND PART OF ABOVE SENTENCES BUT NOT 3UAM
438 4qji - Crystallographic Analysis of the Catalytic Mechanism of Phosphopantothenoylcysteine Synthetase from Saccharomyces cerevisiae 2019 P Zheng, M Zhang, MH Khan, H Liu, Y Jin, J Yue- Journal of molecular, 2019 - Elsevier 4a, b) [14], [15]. Overall structure of the enzymes represent tightly binding dimers linked by dimerization domains which are comprised of three regions as shown in Fig. S4 A divalent metal ion (Ca 2+ in E. coli; Mg 2+ in M. smegmatis. PDB ID: 1U7W; 4QJI ) is coordinated
439 6auj 3ix6, 3gwc Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS) 2019 C Pozzi, L Lopresti, G Tassone, S Mangani- Molecules, 2019 - mdpi.com This review is aimed to summarize the current understanding of structure and function of bTSs and FDTSs and the recent id 1F4B [17]), Brucella melitensis (BmTS; PDB id 3IX6, unpublished research), and Elizabethkingia anophelis (EaTS; PDB id 6AUJ , unpublished research
440 5el0 - An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. 2019 PI Koukos, J Roel-Touris, F Ambrosetti, C Geng- bioRxiv, 2019 - biorxiv.org For the server submission of target 134, we modelled the protein on PDB entry 4d07 and the peptide on 4d07 and 4qh8, threading the target sequence on the peptide structure of the templates 5el0 and followed similar strategies as for target 134. Template-based targets
441 2kok 2mu0 Structure and function prediction of arsenate reductase from Deinococcus indicus DR1 2019 D Chauhan, PA Srivastava, V Agnihotri- Journal of molecular, 2019 - Springer Model1 of ArsC with 3RDW is 1.5 , 1I9D is 2.2 , 1J9B is 2.2 , 2KOK is 3.0 In the case of ArsC, the ArsC C12S mutant ( PDB ID: 1S3C) from E. coli was used as the a confidence score of 0.9040, indicating a very high quality model, where an accurate modeled structure has a
442 4kzk - Structural Flexibility of Peripheral Loops and Extended C-Term Domain of Short Length Substrate Binding Protein from Rhodothermus marinus 2019 JE Bae, IJ Kim, Y Xu, KH Nam - 2019 - preprints.org 120 analysis and substrate docking studies using previously reported crystal structure of SBP ( PDB 121 code 5Z6V) as starting point model structure Among them, 9 models ( PDB code: 123 2QH8, 3LFT, 5ER3, 6DSP, 5BRA, 3KSM, 2DRI, 5DTE, 4KZK , 4RS3, 8ABP) with
443 3rd5 - Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW) 2019 M Jiang, H He, WP Su- Crystals, 2019 - mdpi.com It is worth mentioning that 3RD5 is a test structure with the lowest solvent content that we have successfully applied the direct method to. 4. Methodology After locating the two ligands, MJ and HH were informed that the test structure has the PDB code 4LNW
444 3r9r - Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping 2019 SE Thomas, P Collins, RH James- of the Royal, 2019 - royalsocietypublishing.org purine biosynthesis in maintaining the viability of cells and differences in the structural architecture of bacterial The crystals are similar to those of a previously determined structure of MabPurC with a monomer in the asymmetric unit (figure 1b) ( PDB 3R9R , Seattle Structural
445 3o0m 3lb5, 3oj7, 3r6f Crystal Structure of Histidine Triad Nucleotide-Binding Protein from the Pathogenic Fungus Candida albicans 2019 A Jung, JS Yun, S Kim, SR Kim, M Shin- Molecules and, 2019 - ncbi.nlm.nih.gov 3. The most similar structure was HINT from the protozoal species Leishmania major (LmHINT); the Z-score was 18.8, and the rmsd Species b, C-terminal region, Z-score, RMSD (), Identity (%), C, PDB code, NCBI ID M. smegmatis, II, 14.9, 3.6, 29, 110, 3O0M , WP_011730267.1
446 5u2w - Structure-Guided Generation of a Redox-Independent Blue Fluorescent Protein from mBFP 2019 PW Seo, ES Jo, SH You, DE Cheong, GJ Kim- Journal of molecular, 2019 - Elsevier Structure -guided mutagenesis confirmed the residues' role in the fluorescent capacity of mBFP Moreover, we identified another SDR family protein ( PDB ID 5u2w ) from Burkholderia cenocepacia J2315 (BFPbc) with blue fluorescent capacity in the presence of NADPH, which
447 3kre - NOVEL APPLICATIONS OF SPERMINE AND DERIVATIVES THEREOF 2019 W Pan, W Zhu- US Patent App. 16/334,273, 2019 - freepatentsonline.com Thermotoga maritime (1KUT), Clostridium perfringens (3NUA), Ehrlichia chaffeensis ( 3KRE ), Geobacillus kaustophilus On the basis of the above results, the crystal structure conformations in of Saccharormyces cerevisiae ( PDB : 2CNQ) and Escherichia coli ( PDB : 2GQS) are
448 4tv4 - Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System 2019 F Jiang, N Li, X Wang, J Cheng, Y Huang, Y Yang- Cell, 2019 - Elsevier Overall, the PVC particle displays a simplified structure of the bacterial phage A simplified architecture of T4 phage baseplate lies in the PVC syringe: Pvc5, Pvc7, Pvc8, and Pvc10 form a continuous central spike extending from the inner tube; Pvc11 (D) Initial models of Pvc1, Pvc2, Pvc9 and Pvc11 were built based onPDB: 4TV4, 3J9Q, 2IA7, 5HX2, respectively
449 3dah - Crystal structure of E. coli PRPP synthetase 2019 W Zhou, A Tsai, DA Dattmore- Structural, 2019 - bmcstructbiol.biomedcentral.com Overall, this study details key structural features of an enzyme that catalyzes a critical step in nucleotide metabolism The structure was solved by molecular replacement using the PRPP synthetase from Burkholderia pseudomallei ( PDB 3DAH ) as the search model [14]
450 5k85 - Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle 2019 M Zahn, N Kurteva-Yaneva, J Schuster, U Krug- Journal of molecular, 2019 - Elsevier The substrate specificity of HCL corresponds well to the adenylate-forming active-site architecture ... This is in contrast to other ANL ligase structures, where the CoA or acyl-CoA molecules adopt more stretched conformations, for example, in the thioester-forming conformations of bacterial [38] and fungal acetyl-CoA synthetase (PDB ID: 5K85),
451 4f40 4h7p, 4h51 Leishmania Proteomics: An in Silico Perspective 2019 CA Padilla, MJ Alvarez, A Combariza - 2019 - preprints.org PDB -codes but same structure and proteins with equal structures but elucidated from dif thase from L. major (PGF; PDB ID: 4F40 ) is involved in the lipid metabolic pathway, acting FPPS protein ( PDB ID: 4JZX) is potently inhibited by bisphosphonates in the trypanosomatid
452 3oa1 - Status of antiviral therapeutics against rabies virus and related emerging lyssaviruses 2019 V Du Pont, RK Plemper, MJ Schnell- Current opinion in virology, 2019 - Elsevier RABV drug profiles, past efforts to address the problem and inhibitor candidates identified, and examine how the rapidly expanding structural insight into RABV protein organization has illuminated novel druggable target candidates ... The solved crystal structure for the N0 binding domain is depicted in teal (PDB 3OA1). The solved crystal structure for the dimerization domain is depicted in green and pink with both top and side views...
453 3p0x - Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2 2019 RP Bhusal, W Jiao, BXC Kwai, J Reynisson- Nature, 2019 - nature.com The structural resemblance of the Mtb ICL2 C-terminal domain to members of the GNAT observed in crystal structures of isocitrate-bound ICL1 from Brucella melitensis (Bm ICL1, PDB 3P0X ) of the active site loop are more similar to that found in the crystal structure of substrate
454 4lgv - Molecular Cloning and Exploration of the Biochemical and Functional Analysis of Recombinant Glucose-6-Phosphate Dehydrogenase from Gluconoacetobacter 2019 EJ Ramrez-Nava, D Ortega-Cuellar- International journal of, 2019 - mdpi.com Keywords: glucose 6 phosphate dehydrogenase (G6PD); bioinformatics analysis; kinetic parameters; thermal stability; three-dimensional structure Finally, using homologous 3D structures , we modeled the G6PD protein, which suggests the structural and functional
455 6b4a - A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers 2019 JM Leung, E Nagayasu, YC Hwang, P Pierce, IQ Phan- bioRxiv, 2019 - biorxiv.org Page 5. 5 more in-depth analysis of the conoid fiber architecture , and a comparison of TgDCX and its eight residues 51-128, rmsd 1.905 ); TgDCX ( 6B4A , chain A, aa150-222) vs DCX domains (Figure 5A, Table 1), we used the structure of TgDCX148-243 as a model for
456 6mb1 6maz, 6may, 6mb0 N-myristoyltransferase inhibitor binding mode and phenotype in the malarial parasite. 2019 AC Schlott - 2019 - spiral.imperial.ac.uk lacks myristoylation and instead contains a hydro- phobic N-terminal sequence interacting with the Golgi membrane; its location resembles the distribution of GRASP1, but its structure may result 2010) N-Myristoyltransferase from Leishmania donovani: Structural and Functional ... One of them is the aminomethylindazole series including compounds IMP-0917 (PDB: 5O6H) (Mousnier et al. 2018), and IMP-1002 (PDB: 6MB1) (Schlott et al. 2019)
457 6bfu - Glycosylator: a Python framework for the rapid modeling of glycans 2019 T Lemmin, C Soto- BMC bioinformatics, 2019 - Springer 1 ha0. 5fyl (gp120). 6bfu . Number of sequons. 6 A second N-Acetyl-D-Glucosamine will then be linked through a 1-4 glycosidic bond. Finally, an Alpha-D-Mannosewill be built ab initio and saved to a PDB file The structure of a mannose 9 will be imported as a Molecule instance
458 3sbx - A LONELY GUY protein of Bordetella pertussis with unique features is related to oxidative stress 2019 F Moramarco, A Pezzicoli, L Salvini, R Leuzzi- Scientific reports, 2019 - nature.com first resorted to a theoretical approach. This involved overlapping a model of BP1253 with a monomer of the type-I LOG protein of M. marinum co-crystallized with AMP (MmLOG, PDB 3SBX ) 14,19 . BP1253 was modeled on a
459 3r1i - Structural and biochemical characterization of 20-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32 2019 HL Doden, RM Pollet, SM Mythen, Z Wawrzak- Journal of Biological, 2019 - ASBMB replacement with the structure of an SDR from Mycobacterium marinum ( PDB : 3R1I ) and refined indicate these alanine substitutions did not sig- nificantly affect secondary structural elements (Fig extended N-terminus is important for second- ary and quaternary structure In both
460 3p96 - Targeting the Serine Pathway: A Promising Approach against Tuberculosis? 2019 M Haufroid, J Wouters- Pharmaceuticals, 2019 - mdpi.com Structural differences can occur from one specie to another, ie, human phosphoserine phosphatase is only composed of the PSP domain while of the pathway in order to inhibit the reaction in an allosteric manner (Figure 7b).... Structure of M. avium (3P96) with domain ACT-I in orange, ACT-II in blue, the linker between two ACT domains in red, PSP catalytic domain in grey, linker between PSP domain and ACT-II in green (b). ...
461 2klx - Studies in Computational Biochemistry: Applications to Computer Aided Drug Discovery and Protein Tertiary Structure Prediction 2019 ML Aprahamian - 2019 - rave.ohiolink.edu structures were identified using a receiver operator characteristic (ROC) analysis and a set of known binding compounds. Using these structures as the receptors for structure -based drug discovery, a virtual screen was performed on the National Cancer Institute's ... The six proteins selected from the ab initio set were PDB ID 1tpm, 2klx, 2nc2, 2y4q, 3iql, and 4omo.
462 2klx - Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta 2019 ML Aprahamian, S Lindert- Journal of Chemical Theory and, 2019 - ACS Publications like the following: Which amino acid types provide the most useful structural information structures that served as a nonredundant representation of single chain monomers in the PDB the protein set, distributions of the total number of residues, secondary structure content... The six proteins selected from the ab initio set were PDB ID 1tpm, 2klx, 2nc2, 2y4q, 3iql, and...
463 6c5v - Gammaherpesvirus entry and fusion: A tale how two human pathogenic viruses enter their host cells 2019 BS Mhl, J Chen, R Longnecker- Adv. Virus Res, 2019 - books.google.com 323 Gammaherpesvirus entry and fusion (Waterhouse et al., 2018) based on the crystal structures of EBV gB ( PDB ID: 3FVC), gH ( 6C5V ) and gL The structural sequence alignment of EBV and KSHV gB based on the crystal structure of EBV gB (3FVC)(Backovic et al., 2009
464 6bfu - Glycosylation of viral surface proteins probed by mass spectrometry 2019 AA Hargett, MB Renfrow- Current opinion in virology, 2019 - Elsevier spike GP has 26 NGS with 15 in subunit 1 and 11 in subunit 2 ( PDB : 6BFU ) [89]. (e) Influenza virus hemagglutinin is a homotrimer with 11 NGS ( PDB : 4FNK) [92] can be coupled with other biological data to better understand the role of glycosylation in the structure and function
465 5ts2 3pxu Structural and biochemical studies of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with dephospho-coenzyme A and coenzyme A 2019 A Gupta, PK Singh, P Sharma, P Kaur, S Sharma- International journal of, 2019 - Elsevier pseudolamelli (BpPPAT, PDB ID: 3PXU), Mycobacterium abcessus (MaPPAT, PDB ID: 5O08) and Pseudomonas aeruginosa (PaPPAT, PDB ID: 5TS2 Therefore, structure of enzyme, PPAT must be determined from the bacterium against whom specific drug has to be designed
466 5eqz - Membrane directed expression in Escherichia coli of BBA57 and other virulence factors from the Lyme disease agent Borrelia burgdorferi 2019 KE Robertson, CD Truong, FM Craciunescu, PL Chiu- Scientific reports, 2019 - nature.com All available structures from the genus Borrelia represent proteins expressed without a membrane Towards elucidating structure and function of these critical proteins, we directed translocation of to the outer membrane, Another criterion was the lack of structures in the PDB. RevA has a structure in the PDB33, a 1.80 Å crystal structure (accession no. 5EQZ, unpublished [J.K. Yano, A.H. Sullivan, J. Abendroth, D.D. Lorimer, and T.E. Edwards]), which is of the soluble domain that was expressed in the c
467 3hhj 4dyw Asociacin de genes nudA y htrA de Helicobacter pylori con severidad de patologas gstricas, estudio bioinformtico de la protena NudA. 2019 PA Lincoir Campos - 2019 - repositorio.udec.cl Page 1. Universidad de Concepcin Direccin de Postgrado Facultad de Ciencias Biolgicas - Programa de Magister en Ciencias con Mencin en Microbiologa Asociacin de genes nudA y htrA de Helicobacter pylori con severidad de patologas gstricas
468 3k9w - Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii 2019 A Gupta, PK Singh, N Iqbal, P Sharma- et Biophysica Acta (BBA, 2019 - Elsevier PDB ID: 3ND5; 12), HpPPAT ( PDB ID: 3NV7; 13), BpPPAT ( PDB ID: 3K9W ; 14), CbPPAT ( PDB ID: 4F3R; unpublished), PaPPAT ( PDB ID: 3X1J; 15) and MaPPAT ( PDB ID: 5O06 As indicated by the structure of AbPPAT with CoA ( PDB ID: 5YH7), the ligand binding cleft
469 4g67 4f3n Exceptionally versatilearginine in bacterial post-translational protein modifications 2019 J Lassak, F Koller, R Krafczyk, W Volkwein- Biological chemistry, 2019 - degruyter.com Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. The Mitochondrial Dysfunction protein A (MidA), a PRMT from Dictyostelium discoideum shows structural similarities to the putative protein Q6N1P6 (PDB: 1ZKD) of Rhodopseudomonas palustris and two other hypotheticals (PDB: 4F3N, 4G67) (Baugh et al., 2013) from Burkholderia
470 4npc - Synthesis and antibacterial activity of novel icariin derivatives 2019 A Wang, Y Xu- Die Pharmazie-An International Journal of, 2019 - ingentaconnect.com The X-ray structure of MetAP1 ( PDB : 4npc ) was also obtained from Protein Databank ( PDB ). Before going to the docking procedure, the protein structure was prepared using the Protein preparation wizard of the DS 2017 R2
471 2n6t 2n6s, 2n6w, 2n6x Conditional Prediction of RNA Secondary Structure Using NMR Chemical Shifts 2019 K Zhang, AT Frank- bioRxiv, 2019 - biorxiv.org chemical shifts were downloaded from the Protein Data Bank ( PDB : http://www. pdb .org) and native NMR-derived structure and the comparison structure is the CS-Folding generated structure 2JYM 2L5Z 2LK3 2MIS 2QH2 1Z2J 1JO7 5UZT 2N3Q 5IEM 2L3E 2N6T 2LPS 2N6S
472 3tf6 - Neural networks for improving drug discovery e fficiency 2019 H Hassan Harrirou - 2019 - research-collection.ethz.ch The PDBBind 2018 general set version contains 19588 biomolecu- lar structures , for which some SMILES or FASTA), or full 3D representations of atom coordinates (ie PDB ), with bonds preferable properties of inputs to most machine-learning algorithms: a fixed-size structure
473 4yet 4f2n Tropical and Subtropical Parasitic Diseases: Targets for a New Approach to Virtual Screening 2019 MJR Yunta, RC Dietrich- Molecular informatics, 2019 - Wiley Online Library The most stable extended geometry was always used as the starting structure in all SODb2 (glycosomial), 2GOJ for Plasmodium Falci- parum Fe-SODb1 (cytosolic) and 4YET for Babesia Starting water molecules positions were those published in the corresponding PDB library
474 4odj - Structure of a critical metabolic enzyme: S-adenosylmethionine synthetase from Cryptosporidium parvum 2019 J Ohren, GF Parungao, RE Viola- Section F: Structural Biology, 2019 - scripts.iucr.org Vagin & Teplyakov, 2010) with the structure of C. hominus MetK ( PDB entry 4odj ) as the ordered in the presence of substrates, is disordered and was not modeled in this structure to form functional tetramers with D2 or 222 symmetry, as illustrated by EcoMetK ( PDB entry 1p7l
475 3gwc - Virtual Screening of Novel Potent Molecules Targeting enoyl-ACP reductase as Antitubercular Agents by Molecular Docking studies 2019 V Shivakumar, PM Ramsana, M Risfa- Journal of, 2019 - search.proquest.com Fig 2. Structure and portions nomenclature of linezolid V. Shivakumar et al /J. Pharm. Sci. & Res NO. PDB ID RESOLUTION ENZYMES YEAR 1 2AF6 2.01 Trymidylate synthase 2005 2 2X23 1.80 enoyl-ACP reductase 2010 3 3GWC 1.9 Trymidylate synthase 2009
476 4k9d - Identification and characterization of glyceraldehyde 3-phosphate dehydrogenase from Fasciola gigantica 2019 PB Chetri, R Shukla, T Tripathi- Parasitology research, 2019 - Springer homologs, and the structure of the GAPDH of Brugia Malayi ( PDB ID: 4K9D ) was selected After validation, the modeled structure was used for binding site prediction. The binding site was predicted using the PDB structure co-crystallized with substrate and cofactor (Frayne et al
477 3ief 3m1x, 3mqw, 3m4s Caracterizacin de la protena TV-PSP1 y su posible participacin en la degradacin del RNAm de tvcp39 en Trichomonas vaginalis 2019 AML Villalobos Osnaya - 2019 - repositorioinstitucionaluacm.mx Tabla 4. Expresin de molculas en presencia y ausencia de Fe2+24 Tabla 5. Cdigos de PDB de protenas cristalizadas de la familia PSP26 structure of Tv-PSP1 with a molecular weight of 40.5 kDa. The secondary structure -- The table actually has an error for the 3ief organism :P
478 3ixc - Molecular structure of thermostable and zinc-ion-binding -class carbonic anhydrases 2019 W Wang, Y Zhang, L Wang, Q Jing, X Wang, X Xi- BioMetals, 2019 - Springer are displayed as cartoon diagrams with different colors and are labelled with their respective PDB codes using -TtCA 169 , the 1011 loop is almost the same as 1V67, 1XHD, 2FKO, 3IXC , 4MFG, and However, in the structure of -TtCA 169 , half of the C-terminal -helix is
479 4f0l - Structural and Biochemical Studies of C. jejuni Agmatine Deiminase, E. coli Guanine Deaminase, and S. cerevisiae Guanine Deaminase 2019 R Shek - 2019 - search.proquest.com to uric acid by xanthine oxidase. Figure 1.4. Structure of triose phosphate isomerase. PDB : 6B2W. The beta strands that make up the TIM barrel are shown in red. Page 24. 11 catalyze deamination reactions, the two families differ substantially in their structural architectures. 27
480 6omz - Estudos estruturais e descoberta de ligantes da enzima diidropteroato sintase de Xanthomonas albilineans para o combate da escaldadura das folhas 2019 AA Oliveira - teses.usp.br product) and v. Screening, identification, validation and structural detailing of complexed receptor target structure (SBDD) and the fragment (FBDD) to be applied for tularensis ( PDB 3MCM), Coxiella burnetii ( PDB 3TR9), Mycobacterium smegmathis ( PDB 6OMZ ), Vibrio fischer
481 3u0g 4whx Biochemical and structural insights into PLP fold type IV transaminase from Thermobaculum terrenum 2019 EY Bezsudnova, KM Boyko, AY Nikolaeva, YS Zeifman- Biochimie, 2019 - Elsevier The results of independent MD simulations were qualitatively the same. 2.11. Structural analysis of the fold type IV PLP-dependent enzymes. Proteins which are structurally similar to TaTT were collected from the PDB bank using the structure similarity search module... similar short distance between the tyrosine OH group and the O3 atom of PLP was found in the BCAT structure from Burkholderia pseudomallei (PDB ID: 3U0G, 4WHX).
482 4e98 4iyq Bases estructurales de la sealizacin y regulacin por nitrgeno y procesos asociados. 2019 L Tremio Agull - 2020 - riunet.upv.es PDB : banco de datos de protenas (Protein Data Bank: https://www.rcsb.org/ pdb /home/home. do) PEG 49 Captulo 1: Studies on cyanobacterial protein PipY shed light on structure , potential functions Functional and structural studies in bacteria ----- 117
483 2mj3 - Evolutionary relationships between low potential ferredoxin and flavodoxin electron carriers 2019 IJ Campbell, GN Bennett, JJ Silberg- Frontiers in Energy Research, 2019 - frontiersin.org This bioinformatic study highlights understudied PECs whose structure , stability, and partner specificity should be 1CZP, 2WLB, 3LXF, 1B9R, 1UWM, 1PDX, 1M2D, 1I7H, 3AH7, 2MJD, 2MJ3 , 2Y5C, 5FFI For Flds, we used PDB IDs 2FZ5, 1FLD, 4HEQ, 2HNA, 2FX2, 3F6R, 3KAP
484 3nfw - The oxygen reduction reaction catalyzed by Synechocystis sp. PCC 6803 flavodiiron proteins 2019 KA Brown, Z Guo, M Tokmina-Lukaszewska- Sustainable Energy &, 2019 - pubs.rsc.org 3, 12 and 13) and provide more insights into the Flv structure , substrate reactivity and protein based on heuristics to maximize confidence, percentage identity and alignment coverage ( PDB IDs: 1VME for the oxidoreductase domain: 5ZC2, 55 3RH7, 4HX6, 56 3K87, 57 3NFW 58
485 3k2c - Supplementary material to GISA: Using Gauss Integrals to identify rare conformations in protein structures 2019 C Grnbk, T Hamelryck, P Rgen - 2019 - biorxiv.org The rar2 scoring method scans for structures having a distribution of words significantly different from that found in the old, here set to 7 ngstrm; the E chain of the 2er7 structure is disqualified for this reason, but 7> means that in the PDB -file the chain id was left blank 14
486 3qhd 3p0z, 3P0Z Design, synthesis, and evaluation of potential Burkholderia pseudomallei IspF inhibitors 2019 S Watkins - 2019 - commons.lib.niu.edu xvi nOe Nuclear Overhauser enhancement/nuclear Overhauser effect PDB Protein Data Bank Pf Plasmodium falciparum ppm Parts per million RST Relative saturation transfer SAR Structure activity relationship SSGCID Seattle Structural Genomics Center for Infectious Disease ... It is possible the sp2 N of the imidazole is binding to the Zn2+, as seen in the crystal structures of 88 in BpIspF (3P0Z, 3QHD).
487 4qfh 4gie, 4g7f Insights into Ergosterol Peroxide's Trypanocidal Activity 2019 T Meza-Menchaca, A Ramos-Ligonio- Biomolecules, 2019 - mdpi.com \To identify potential Tc proteins that might directly interact with ergosterol peroxide, an inverse-docking screening was performed on a subset of Tc protein crystallography structures.. Table 1. The best matches between T. cruzi proteins and ergosterol peroxide in descending order of ∆G predictive value ... Dihydroorotate dehydrogenase 4QFH 3W1R −9.1 −11.17 6.407
488 5ve7 - Crystal structure of UDP-glucose pyrophosphorylase from Yersinia pestis, a potential therapeutic target against plague 2019 ME Gibbs, GT Lountos, R Gumpena- Section F: Structural, 2019 - scripts.iucr.org A over 278 aligned residues, 72% sequence identity), Burkholderia ambifaria ( PDB entry 5ve7 ; rmsd of 1.3 A over 275 aligned residues, 52% sequence identity), Helico- bacter pylori ( PDB entry 3juk Figure 1 (a) Stereoview of a cartoon representation of the crystal structure of Y
489 4e51 - Incorporation de la beta alanine dans des polypeptides 2019 G Nigro - 2019 - tel.archives-ouvertes.fr 89 I. 2 Structures de la MetRS cocristallise avec des analogues de la mthionine : Sites de reconnaissance des acides aminés de trois AARS de classe II. A : HisRS de Burkholderia thailandensis (4E51), B :
490 6mfk - Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species 2019 A Alcala, G Ramirez, A Solis, Y Kim, K Tan- Protein, 2019 - Wiley Online Library from P. aeruginosa ( PDB IDs: 1XAT, 2XAT7) and E. anophelis ( PDB ID: 6MFK ). Known SAT 1(A)]. When we compared our structures of the Vibrio proteins with CATs and SATs from the PDB , we found the The AfCAT structure had
491 3u0d - The structure of the bacterial ironcatecholate transporter Fiu suggests that it imports substrates via a two-step mechanism 2019 R Grinter, T Lithgow- Journal of Biological Chemistry, 2019 - ASBMB TBDTs are highly divergent in sequence but share a common structural architecture , consisting of a 22 The structure of Fiu consists of a 22-stranded transmembrane -barrel characteristic of the DALI web server (37) identified PiuA from Acinetobacter baumannii ( PDB code 5FP1
492 6cw5 - Unraveling structural insights of ribokinase from Leishmania donovani 2019 S Gatreddi, V Pillalamarri, D Vasudevan- International journal of, 2019 - Elsevier Z-score 42.3; rmsd 2.1 for 307 C atoms), C. neoformans ( PDB ID: 6CW5 , Z-score 36.5; rmsd 2.7 for 290 C atoms) and adenosine kinase of A. tumefaciens ( PDB ID: 2RBC of a five amino acid stretch was observed at the two positions in the primary structure of LdRK
493 4xk1 - N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica 2019 RK Singh, P Tomar, S Dharawat, S Kumar- International journal of, 2019 - Elsevier 3. Comparative analysis, using the RAPIDO server, of PSAT structures from various organisms with the EhPSAT structure . PDB IDs, Sequence identity (%), RMSD with EhPSAT monomer in (number of residues compared) 4XK1 (P. aeruginosa) [38], 40, 1.52 (for 337 residues)
494 3h7f - Combinatorial Designing of Novel Lead Molecules Towards the Putative Drug Targets of Extreme Drug-Resistant Mycobacterium tuberculosis: A Future Insight for 2019 N Bachappanavar, S Skariyachan- Essentials of Bioinformatics, Volume II, 2019 - Springer glyoxylate and dicarboxylate. The native structure of serine hydroxymethyltransferase ( PDB ID: 3H7F ) possessed two chains (A and B) with molecular weight of 95226.08 Da and a resolution of 1.5 (R-value free, 0.196) (Fig. 12.2a). Further
495 4g7f - Caracterizacin de la respuesta inmunolgica en el modelo murino inmunizado con la rTcENo por va subcutnea 2019 M Gutirrez Soto - 2019 - repositorioinstitucional.buap.mx Agarosa NTD Enfermedades Tropicales Desatendidas OMS Organizacin Mundial de la Salud ONU Organizacin de las Naciones Unidas OPS Organizacin Panamericana de la Salud PBS Buffer salino de fosfatos PBS-T Buffer salino de fosfatos-Tween 20 PDB Banco de
496 4hvt 5tnx, 3s6m SPOT-peptide: Template-based prediction of peptide-binding proteins and peptide-binding sites 2019 T Litfin, Y Yang, Y Zhou- Journal of chemical information and, 2019 - ACS Publications test set taken from another structure -based peptide-binding site predictor, SPRINT- peptide11 Structural genomics targets (SG4444) 11,813 proteins involved in structural genomics studies were collected from the PDB plate primarily based on domain-level structural similarity
497 4odj - Genomewide analysis of mode of action of the S-adenosylmethionine analogue sinefungin in leishmania infantum 2019 A Bhattacharya, M Sharma, C Pakkinathan, BP Rosen- Msystems, 2019 - ncbi.nlm.nih.gov C (B) The human LCMT1-PP2AC structure is presented SNF is a structural analogue of S-adenosylmethionine (AdoMet), a key methyl group donor to a
498 4l82 - Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) 2019 R Fallahzadeh, B Bambai, K Esfahani, AA Sepahi- Heliyon, 2019 - Elsevier their PDB information, the multiple alignments of these 22 PDB files was done with the DszD. pdb (Fig 1. Predicted three dimensional structure for wild-type DszD enzyme residues (Asn or Ile residue instead of Ala79) were presented on the 3K88 and 4L82 homologous proteins
499 5i7w - Omega transaminases: discovery, characterization and engineering 2019 CM Palacio - 2019 - rug.nl (7), who grouped the enzymes in superfamilies by structural similarities and named the superfamilies after the PLP enzyme of which the crystal structure was determined first. The PLP fold-type classification system of Grishin et al Brucella suis, pdb 5I7W )
500 3gqt - Design, Synthesis, and Biological and In Silico Study of FluorineContaining Quinoline Hybrid Thiosemicarbazide Analogues 2019 DB Patel, KD Patel, NP Prajapati- Journal of, 2019 - Wiley Online Library Thus, design, development, and structure modification existing drugs are necessary with highly selective potency on specific strains Entry, Code no. R 1, R 2, R 3, Product, Yield (%)a a Purified yield. 1, 8a, 4CF 3, 6CF 3, ... Figure 4c describes the interaction details of compounds 8d and 8k with PDB: 3GQT; compound 8d showed four H‐bond interactions
501 4fi5 - Identification and validation of specific B-cell epitopes of hantaviruses associated to hemorrhagic fever and renal syndrome 2019 F de Paiva Conte, BC Tinoco, TS Chaves- PLoS Neglected, 2019 - ncbi.nlm.nih.gov 1) was performed against the expasy SWISS-MODEL template server [26][2][2]. Three structures were selected ( PDB ID: 5E04, 5FSG, 4FI5 ) with the The lowest energy model was selected using PyMOL Version 1.8 and your 3D structure evaluated with Verify 3D [29, 30
502 3ix6 - Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis 2019 B Pandey, S Grover, J Kaur, A Grover- Scientific reports, 2019 - nature.com crystal structures of the ThyA enzyme in Brucella melitensis (PDBID: 3IX6 ), M. tuberculosis 3QJ7) 20 , Enterococcus faecalis ( PDB IF: 6QYA), and Escherichia coli ( PDB ID: 1AXW Comparative analysis of the binding free energy, secondary structure elements, and free energy
503 3pk0 3rih Structural and functional characterization of the aminoacetone utilization microcompartment from Mycobacterium smegmatis MC2 155 2019 E Mallette - 2019 - atrium.lib.uoguelph.ca P)(H) - nicotninamide adenine dinucleotide (phosphate)(reduced) NTP - nucleotide triphosphate PDB - protein data bank (protein structure archive) PDU 1.2.1 Superstructure Architecture Microcompartments were first visualized in electron micrographs of carboxysome
504 3k2c - The Schistosoma mansoni cyclophilin A epitope 107-121 induces a protective immune response against schistosomiasis 2019 TT de Melo, MM Mendes, CC Alves, GB Carvalho- Molecular, 2019 - Elsevier The resulting structure was predicted using six templates (4I9Y: e3 sumo-protein ligase Cyclophilin from Homo sapiens, variant A; 1IHG: bovine cyclophilin 40, 3K2C : peptidyl-prolyl cuniculi; 1XO7: Cyclophilin from Trypanosoma cruzithe bovine Cyclophilin 40 ( PDB code: c1ihgA
505 3tde 3iml, 3s82, 3rv2 Toward an Enzyme-coupled, Bioorthogonal Platform for Methyltransferases: Probing the Specificity of Methionine Adenosyltransferases 2019 TD Huber - 2019 - uknowledge.uky.edu 4.4.5 Protein crystallization, data collection, and structure refinement ..... 105 reported similar promiscuity for the archael Sulfolobus solfataricus MAT (sMAT) and, notably, the corresponding first structural elucidation for a thermostable MAT (sMAT, PDB ID 4HPV)
506 2kok - A deep learning approach to the structural analysis of proteins 2019 M Giulini, R Potestio- Interface focus, 2019 - royalsocietypublishing.org Second, we show that the application of a simple, standard and computationally not expensive DL architecture to the selected features gives satisfactory results, suggesting that The raw data employed in the present work, including PDB files, protein structure datasets, CNN ... Eigenvalues associated with 2KOK, 2YQD, and 1MEK were predicted with reasonable accuracy, the overall average MAPE being 30.7, 35.5 and 48.3, respectively.
507 3uf8 - Carotenoids Overproduction in Dunaliella Sp.: Transcriptional Changes and New Insights through Lycopene Cyclase Regulation 2019 F Elleuch, HB Hlima, M Barkallah, P Baril, S Abdelkafi- Applied Sciences, 2019 - mdpi.com and cytochrome b 6 /f complex and maintains the integrity of cell architecture [7]. It attempted to understand how this stress could affect LCYB molecule by generating its 3D structure to 200 bp, chosen temperature (Tm) around 60 C, and avoiding secondary structures and self
508 3qhx - SolXplain: An Explainable Sequence-Based Protein Solubility Predictor 2019 R Mall- bioRxiv, 2019 - biorxiv.org be used as a scoring function to measure the quality of a tree structure Ht at in [13], devise a fast, greedy and iterative algorithm to identify these optimal tree structures We train our XGBoost classifier on top of physio-chemical (global), sequence and structural features extracted
509 4hvt - Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase 2019 K Ellis-Guardiola, H Rui, RL Beckner, P Srivastava- Biochemistry, 2019 - ACS Publications Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase While extensive structural characterization of bacterial and mammalian POPs has been performed, no structures for archaeal POPs have been reported
510 5cy4 - Structural basis of small RNA hydrolysis by oligoribonuclease (Cps ORN) from Colwellia psychrerythraea strain 34H 2019 CW Lee, SH Park, CS Jeong, SS Cha, H Park- Scientific reports, 2019 - nature.com Structure alignment search using DALI server showed that CpsORN exhibited high structural similarity with ORN HinORN; PDB code 1J9A), and Acinetobacter baumannii (AbaORN; PDB code 5CY4 ), and XC847 from Xanthomonas campestris (XcaORN; PDB code 2GBZ
511 4qhq - Navigating Among Known Structures in Protein Space 2019 A Narunsky, N Ben-Tal, R Kolodny- Computational Methods in Protein, 2019 - Springer evolutionary history, with sequences that diverged beyond the point where one can identify their common ancestry; for example, the SCOP fold, CATH Architecture , and ECOD As both neighbors ( pdb 4qhq and pdb 3qwl) have a bound methionine in their PDB structure (Fig
512 3nwo - Integration of bioinformatics analysis and experimental biocatalysis for a comprehensive approach to the synthesis of renewable polyesters 2019 M CESPUGLI - 2019 - arts.units.it the structural features of a dataset of serine hydrolases, where cutinases play a central role enzyme structure , and the catalytic triad is represented by Ser105, Asp187 and His224. The This molecular architecture is responsible for the reduction of molecular oxygen by the
513 6d9y 6d9n Protein secondary structure online server predictive evaluation 2019 - Chinese Journal of Bioinformatics, 2019 - search.ebscohost.com 1 SPIDER Fig.1 Main structure of SPIDER 2.1
514 2kn9 - Structure Based Computational Exploration of Beilschmiedia Compounds with Selected Targets against Multidrug-Resistant Mycobacterium tuberculosis 2019 M Yasir, P Singh, S Chohan, R Shrivastava- INDIAN JOURNAL OF, 2019 - ijper.org Protein Name PDB - ID Binding Energy (kcal/mol) Antigen 85C 1dqz -3.34 Cytochrome P450 Crystal structure of 3-bromopyruvate modified isocitrate lyase (icl) 1f8m -2.09 EmbR 2ff4 -4.38 Hydroxymycolate synthase MmaA4 2fk7 - Zinc-substituted rubredoxin B 2kn9 -3.46 Cell
515 4djt - PatchSearch: a web server for off-target protein identification 2019 J Rey, I Rasolohery, P Tuffry, F Guyon- Nucleic acids, 2019 - academic.oup.com 4djt 22.3 0.376 positive 10.378 The patch was extracted around ADP in the 1lkx myosin structure . Structural similarities between the patch and the entire surface of 40 PDB structures known to be able to interact, ie 'positive', or not, 'negative', with ADP or similar ligands
516 4pfz 3qdf, 3rr6 Structural and functional analysis of a dimeric fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum 2019 W Yoo, CW Lee, B Kim, LTHL Le, SH Park- Biochemical and, 2019 - Elsevier overall monomer structure , a schematic diagram of the connectivity, and the residue numbering of each secondary structure are shown in ID:3RR6, Z score: 34.6), a 5-carboxymethyl-2- hydroxymuconate delta-isomerase from Mycobacterium smegmatis ( PDB ID: 4PFZ ; Z score
517 2lbb 2l4b Physical Folding Codes for Proteins 2019 X Ma, C Hou, L Shi, L Li, J Li, L Ye, L Yang- arXiv preprint arXiv, 2019 - arxiv.org 15 Soares, CM, Teixeira, VH & Baptista, AM Protein Structure and Dynamics in Nonaqueous Solvents: Insights from Nature Structural Biology 10, 980, doi:10.1038/nsb1203-980 (2003 JL The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
518 6n38 - Baseplate component TssK and spatio-temporal assembly of T6SS in Pseudomonas aeruginosa 2019 D Liebl, M Robert-Genthon, V Job, V Cogoni- Frontiers in, 2019 - frontiersin.org TssE is the structural homolog of the T4 phage baseplate components gp25 (Leiman et al To confirm that TssK and TssE assemble into the same spot-like structure we generated and Mekalanos, 2012; Vettiger and Basler, 2016), very low number of TssB- structures were seen... The TssK oligomers disassemble upon action of PppA (shown in dashed lines). Stoichiometry (TssK3)2(TssF2/TssG) in accordance with cryo-EM structure (PDB 6N38) is shown.
519 3i0p - Gene encoding a novel enzyme of LDH2/MDH2 family is lost in plant and animal genomes during transition to land 2019 LV Puzakova, MV Puzakov, AA Soldatov- Journal of molecular evolution, 2019 - Springer Prediction of structure and properties of the discov- ered enzyme identified the highest homology to 3I0P pro- tein (P Although tertiary struc- ture of 3I0P protein (malate dehydrogenase from Entamoeba histolytica, https ://doi.org/10.2210/pdb3i 0p/ pdb ) and 1V9N
520 3rr2 - Insights into multifaceted activities of CysK for therapeutic interventions 2019 P Joshi, A Gupta, V Gupta- 3 Biotech, 2019 - Springer PDB ID (References) 3RR2 (Baugh et al A recent study where a natural A241V variant of S. flexneri CysE has unstable quaternary assembly and reduced activity, suggests transient dissociation of quaternary structure of CysE to be another regulatory mechanism for cysteine
521 5u29 - Sntese, elucidao estrutural e estudos in silico de novos compostos 2-amino-tiofnicos imdicos candidatos a frmacos antifngicos, antileishmanicida e 2019 ALC Pereira - 2019 - repositorio.ufpb.br Synthesis, structural elucidation and in silico studies of novel 2-amino- thiopheneic compounds imidic hybrids were synthesized with determined physicochemical characteristics and confirmed structures through 1H CYP51A1 ( PDB id: 1EA1); (B): ESBT-06 e FTAs ( PDB id: 3SFX
522 4f2n - Antileismanial activity, mechanism of action study and molecular docking of 1, 4bis (substituted benzalhydrazino) phthalazines 2019 AH Romero, N Rodrguez, H Oviedo- Archiv der, 2019 - Wiley Online Library candidate for further pharmacokinetic and in vivo experiments as antileishmanial agent, and as a platform for further structural optimization ... Representation of molecular docking of 1,4‐bis‐(substituted benzalhydrazino) phthalazine 3b on the superoxidedismutase active sites of Leishmania major (PDB code: 4F2N)
523 5cy4 - Structural insights into nanoRNA degradation by human Rexo2 2019 LY Chu, S Agrawal, YP Chen, WZS Yang, HS Yuan- RNA, 2019 - rnajournal.cshlp.org 6A4E), or deposited in the protein data bank, including those from E. coli ( PDB codes: 1YTA, 2IGI), Acinetobacter baumannii ( PDB code: 5CY4 ), and Haemophilus influenzae ( PDB code 1J9A) Structural coordinates and diffraction structure factors of Rexo2-RNA, Rexo2-DNA1
524 3men - Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery 2019 V Chahal, S Nirwan, R Kakkar- Physical Sciences Reviews, 2019 - degruyter.com Figure 2: Steps involved in homology modeling for 3D structure prediction sequences of proteins with known 3D structures available in various depositories such as PDB , using the In some cases, a single template is not enough to provide the complete structural information ... This catalytic domain was modeled using the I-TASSER server [98] by exploiting the solved crystal structures of some HDAC proteins having structural identities (2VCG (37%), 1ZZ0 (37%), 1C3P (29%), 3MEN (36%), 3COY (47%),
525 3oj6 4o3v, 6cuq Combining statistical and neural network approaches to derive energy functions for completely flexible protein backbone design 2019 B Huang, Y Xu, H Liu- bioRxiv, 2019 - biorxiv.org To design a backbone, an intended framework is specified first. This framework defines at a very coarse level the intended backbone architecture , including the numbers For each native structure with the given PDB ID, results of four simulations are plotted in different
526 4f2n - Crystal structure of an iron superoxide dismutase from the pathogenic amoeba Acanthamoeba castellanii 2019 O Dao, K Asaithambi, BK Na, KH Lee- Section F: Structural Biology, 2019 - scripts.iucr.org et al., 2014), P. falciparum ( PDB entry 2bpi; Boucher et al., 2006) and L. major ( PDB entry 4f2n ; Phan et al., 2015) and of MnSOD from Homo sapiens ( PDB entry 5vf9 architecture of AcFeSOD is similar to those of other Fe/MnSODs, including the E. coli FeSOD structure (Fig
527 4whx 3u0g Functional characterization of PLP fold type IV transaminase with a mixed type of activity from Haliangium ochraceum 2019 YS Zeifman, KM Boyko, AY Nikolaeva- et Biophysica Acta (BBA, 2019 - Elsevier These results complement our knowledge of the catalytic diversity of transaminases and indicate the need for further research to understand the structural basis of substrate specificity in these enzymes. Abbreviations PDB entry code, 6H65. 2.8. Structure solution and refinement
528 3sbx - Atypical LONELY GUY protein in Bordetella pertussis synthetizes a cytokinin-like compound negatively related to oxidative stress 2019 F Moramarco - 2019 - amsdottorato.unibo.it BP1253 and LOGs, while Cluster omega to realize amino acid sequence alignment with specific type-I and type-II LOGs. The structural analysis were performed through PDB Viewer, either to develop the modeling of BP1253 that to determinate the coordinates of ... Characteristic of this M. marinum protein with PDB ID 3SBX is that it was crystallized in complex with AMP
529 3i44 - Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the 2019 S Malhotra, AF Alsulami, Y Heiyun, BM Ochoa, H Jubb- PloS one, 2019 - journals.plos.org We modeled the structure the transmembrane domain and the missing regions between the kinase domain and the transmembrane residue range: 191239, using ( PDB IDs: 1H4I, 3I44 , and 1H4J) as We then mapped the mutation data on to the modeled structure (Fig 6A)
530 6nb7 6nb4 Molecular mechanism for antibody-dependent enhancement of coronavirus entry 2019 Y Wan, J Shang, S Sun, W Tai, J Chen, Q Geng- Journal of, 2019 - Am Soc Microbiol change of the spike. Future study on the high-resolution cryo-EM structure of MERS- 230 CoV Se trimer complexed with Mersmab1 will be needed to provide detailed structural 231 information for the Mersmab1-triggered conformational changes of MERS-CoV Se. SARS-CoV S-e complexed with S230 mAb (PDB ID: 6NB7).
531 4dhe 6n38 Assembly and subcellular localization of bacterial type VI secretion systems 2019 J Wang, M Brodmann, M Basler- Annual review of microbiology, 2019 - annualreviews.org The TssM cytosolic domain is modeled after NTPase-like domain EngB ( PDB 4DHE ) followed by a helical extension modeled after DPY-30 f ) Structure of the PDB 3ZRJ) binding to the TssC positioned in the same orientation as in panel e. Abbreviation: PDB , PDB , Protein Data
532 4nbr - SCOT: Rethinking the Classification of Secondary Structure Elements 2019 T Brinkjost, C Ehrt, O Koch, P Mutzel- Bioinformatics, 2019 - academic.oup.com -bulge which leads to a kinked (highlighted in green) -helical structure in 4nbr @ pdb (chain A for SCOT and SHAFT for the structure pair 4k20@ pdb and 5cna@ pdb results from based assignment methods except for SHAFT are the most robust ones regarding structure quality
533 4yk1 4yk3, 4yk2 Versatility of the BID domain: Conserved function as type-IV-secretion-signal and secondarily evolved effector functions within Bartonella-infected host cells 2019 A Wagner, C Tittes, C Dehio- Frontiers in microbiology, 2019 - frontiersin.org BID fold is highlighted through superposition of the three solved BID domains: BroBep6_tBID1 (green; PDB : 4YK1 ), BclBep9_tBID1 (cyan; PDB : 4YK2), and BheBepE_BID1 (purple; PDB : 4YK3 into ancestral tBIDs found in the canonical FIC-OB-BID architecture and derived
534 6d8w 6n41 Computationally optimized broadly reactive vaccine based upon swine H1N1 influenza hemagglutinin sequences protects against both swine and human isolated 2019 AL Skarlupka, SO Owino- Human vaccines &, 2019 - Taylor & Francis The known crystal structure were used for A/California/07/2009 ( PDB accession: 3lzg23) and A/Swine/Indiana/P12439/2000 templates were chosen for model building.29 The crystal struc- tures of A/Jiangsu/ALSI/2011 (H1N1) HA ( PDB accession: 6d8w ) was selected
535 3r20 3r8c Homology modeling and in silico toxicity assessment of potential inhibitors of cytidylate kinase from Mycobacterium tuberculosis 2019 MA Isa- Network Modeling Analysis in Health Informatics and, 2019 - Springer Six templates ( PDB CODE: 3R20 , 3R8C, 1Q3T, 1CKE, 2CMK, and 4E22) were selected based on the An alignment of the CMK and the 3R20 revealed that their structures share a 74.0 Ten structural models of CMK were generated, and the structure with the least DOPE and fold
536 4k73 - Structural Basis for the Interaction and Processing of -Lactam Antibiotics by l,d-Transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis 2019 GA Libreros-Ziga, C dos Santos Silva- ACS Infectious, 2019 - ACS Publications Structural Basis for the Interaction and Processing of -Lactam Antibiotics by l,d-Transpeptidase 3 These structures revealed a fold and catalytic diad similar to those of other Ldts Mt The Ldt Mt3 faropenem structure indicated that faropenem is degraded after Cys-246 acylation The phases were obtained by molecular replacement with Phaser53 from CCP4 suite,54 adopting the PDB entries 4K73 and 5DU727 as models for LdtMt3 and LdtMt5 structures, respectively
537 3quv - Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification 2019 SE Thomas, AJ Whitehouse, K Brown, JM Belardinelli- bioRxiv, 2019 - biorxiv.org at 1.67 and 1.48 resolution respectively ( PDB codes 6NW6 & 6NW7). The crystals belong 109 region is largely disordered, with residues 162-177 not clearly visible in the apo structure 115 of a deep trefoil knot architecture , made of three distinct untwisted loop regions
538 4o3v - Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis 2019 I Tuvi-Arad, G Alon- Journal of cheminformatics, 2019 - jcheminf.biomedcentral.com model of allostery (also referred to as the symmetry model) [5]. Synthesizing a symmetric structure requires less is a characteristic of many protein structures [7]. Searching the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB ) [8, 9] for
539 6axe 4ex4 The glyoxylate shunt as a target for antibacterial intervention in Pseudomonas aeruginosa 2019 AC McVey - 2019 - aspace.repository.cam.ac.uk The structure of MSG from four prokaryotic species has been resolved by X-ray crystallography: E. coli... Mycobacterium marinum (PDB entry 6AXE), and Mycobacterium leprae (PDB entry 4EX4). Also, the E. coli MSG structure has been solved by NMR
540 4lgv - Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress 2019 GA Ellis, WP Klein, G Lasarte-Aragones, M Thakur- ACS, 2019 - ACS Publications Within each material class of scaffolds, attention is given to their inherent chemical diversity, how they are engineered, how they allow for enzymatic attachment, their ease of use, their benefits (eg, inherent three-dimensional architecture ) ... Illustration of the proposed channeling complex using a poly(lysine) bridge as an electrostatic surface between hexokinase (HK) (PDB entry 3VF6) and glucose-6-phosphate dehydrogenase (G6PDH) (PDB entry 4LGV).
541 5vm1 - Heterologous expression and biochemical characterization of a thermostable xylulose kinase from Bacillus coagulans IPE22 2019 Y Zhang, C Zhao, Z Ni, M Shao, M Han- Journal of basic, 2019 - Wiley Online Library was shown in Figure 1. In the 3D structure modeling analysis, Bc-XK showed the highest sequence identity of 35% with the homologue from Brucella ovis ATCC 25840 ( PDB accession number 5VM1 , DOI: 10.2210/pdb5VM1/ pdb ), the confi- dence and structure coverage values
542 3tde 3iml, 5t8s The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase 2019 D Kleiner, F Shmulevich, R Zarivach, A Shahar- Journal of molecular, 2019 - Elsevier MAT ( PDB ID), Phylum/class, Monomer length b, % sequence identity to E. coli, Interface c, M. tuberculosis ( 3TDE ), Actinobacteria/actinobacteria, 403, 59%, large, 11.5, 1983, 23, 11 1). In addition, the flexible loops (positions 89116) fully discernible in this structure were found
543 3kre - COMPOUNDS WEAKENING SAICAR SYNTHETASE ACTIVITY AND APPLICATIONS 2019 W Pan, W Zhu- US Patent App. 16/334,256, 2019 - freepatentsonline.com 3R9R), Thermotoga maritime (1KUT), Clostridium perfringens (3NUA), Ehrlichiachaffeensis ( 3KRE ), Geobacilluskaustophilus (2YWV basis of the above results, the crystal structure conformations in Saccharormyces cerevisiae ( PDB : 2CNQ) and Escherichia coli ( PDB : 2GQS)
544 4pq9 - A subfamily roadmap for functional glycogenomics of the evolutionarily diverse Glycoside Hydrolase Family 16 (GH16) 2019 AH Viborg, N Terrapon, V Lombard, G Michel- Journal of Biological, 2019 - ASBMB by the presence of numerous helical elements on the core -jelly-roll fold, two in the N-terminal region and four in the C- terminal region, most of which are located on the opposite side of the structure from the active A tryptophan (W154 in PDB ID 4PQ9 (unpublished)) present
545 4wi1 - Drug targeting of one or more aminoacyl-tRNA synthetase in the malarial parasite Plasmodium falciparum 2018 M Yogavel, R Chaturvedi, P Babbar, N Malhotra- Drug discovery today, 2018 - Elsevier HF, yellow PDB ID: 4YDQ), glyburide (violet, PDB ID: 5IFU), TCMDC-124506 (orange, PDB ID: 4WI1 ) and modeled Takeda compound B (green, PDB ID: 5VAD Among these, benzoxaboroles target the editing site of Pf-LRS cyto effectively and the crystal structure for the
546 3ily - Virtual Screening Studies for Discovery of Novel Inhibitors of Inflammatory Process Targets 2018 MT Scotti, MF Alves- Current, 2018 - ingentaconnect.com The structure -based pharmacophore models were produced with several inhibitor complexes (3PDC, 31 3ANS, 27 3ANT, 3OTQ, 3KOO, 3ILY , 3I28, 1ZD5 and 1VJ540) from the PDB databank (https://www.rcsb.org/ pdb /) [139-144]
547 5jry - Molecular Mechanisms of Bacterial Bioluminescence 2018 E Brodl, A Winkler, P Macheroux- Computational and Structural, 2018 - Elsevier we also show stick models of the substrate analog (indole-3-acetaldehyde – blue) and the cofactor (NADP+ − grey) in the respective binding sites obtained from the superposition of the LuxC model with indole-3-acetaldehyde dehydrogenase from Pseudomonas syringae (PDB 5IUW) and from the structure of an aldehyde dehydrogenase from Burkholderia multivorans (PDB 5JRY), respectively.
548 5b8i - In Vitro and In Vivo Assessment of FK506 Analogs as Novel Antifungal Drug Candidates 2018 Y Lee, KT Lee, SJ Lee, JY Beom- Antimicrobial agents, 2018 - Am Soc Microbiol However, the structure of the fungal ternary complex from Coccidioides immitis has recently been reported ( PDB accession number 5B8I ), which would facilitate the rational design of FK506 analogs that can discriminate human and fungal calcineurins
549 4wi1 4olf Inverse docking based screening and identification of protein targets for Cassiarin alkaloids against Plasmodium falciparum 2018 A Negi, N Bhandari, BRK Shyamlal- Saudi Pharmaceutical, 2018 - Elsevier In order, to find the active site on those structure which does not contain co-crystallise ligand, active site finder tool was used to identify the active patches Protein, PDB , Res 4WI1 , 1.65, 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]-urea, 0.501
550 4ggq - Enzyme targets for drug design of new anti-virulence therapeutics 2018 CM Kahler, M Sarkar-Tyson, EA Kibble- opinion in structural, 2018 - Elsevier Mip from Burkholderia pseudomallei as a complex with a pipecolic acid derivative (CJ40) ( PDB : 4GGQ ) d) Ribbon diagram of the structure of EptA ( PDB : 5FGN a detailed understanding of the mechanism of substrate binding and catalysis will enable a structure guided approach
551 4q14 - Diatom allantoin synthase provides structural insights into natural fusion protein therapeutics 2018 J Oh, A Liuzzi, L Ronda, M Marchetti- ACS chemical, 2018 - ACS Publications Diatom Allantoin Synthase Provides Structural Insights into Natural Fusion Protein Therapeutics The 1.85--resolution crystal structure of allantoin synthase from the diatom Phaeodactylum tricornutum provides a rationale for the domain combinations observed in the metabolic The 1.85-Å-resolution structure of PtAlls was determined by molecular replacement program in PHENIX(55) by using the Urah structure from Brucella melitensis (PDB ID: 4Q14) as a search model.
552 3oc6 - Biochemical Characterization and Structural Modeling of Fused Glucose-6-Phosphate Dehydrogenase-Phosphogluconolactonase from Giardia lamblia 2018 L Morales-Luna, H Serrano-Posada- International journal of, 2018 - mdpi.com Recent Trends and Applications of Molecular Modeling in GPCRLigand Recognition and Structure -Based Drug Design. Choose your preferred view mode Giardia lamblia. G6PD. purification. recombinant expression. bioinformatics analysis. three-dimensional structure
553 4wxt - Inhibition of thioredoxin A1 from Corynebacterium pseudotuberculosis by polyanions and flavonoids 2018 RJ Eberle, LA Kawai, FR de Moraes, D Olivier- International journal of, 2018 - Elsevier The initial model of the Cp-TrxA1 protein was obtained by homology modeling with the M. avium Trx structure ( PDB : 4WXT ; 50% homology), in order to Structural superposition of the Cp-TrxA1 homology model and the M. avium Trx structure showed a RMSD of 0.188 (Fig
554 5umf 3fdz CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii 2018 E Filippova, AS Halavaty, G Minasov- Frontiers in cellular, 2018 - eprints.whiterose.ac.uk Crystallography revealed insights into the overall structure , protein oligomeric states and molecular details of active sites important for ligand recognition The targets studied herein were crystallized and their structures characterized, as structural studies have
555 5if3 - Semi-rational engineering of carbonyl reductase YueD for efficient biosynthesis of halogenated alcohols with in situ cofactor regeneration 2018 M Naeem, AU Rehman, B Shen, L Ye, H Yu- Biochemical Engineering, 2018 - Elsevier Modeller 9.12 package on the basis of the crystal structure of a short-chain dehydrogenase/ reductase SDR ( PDB ID: 5if3 ) from Burkholderia amino acid residues for site directed mutagenesis, docking of the model substrate 3-bromoacetophenone into the structure of YueD
556 4p8r 4lsm Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa 2018 ATP Machado, M Silva, J Iulek- et Biophysica Acta (BBA)-Proteins and, 2018 - Elsevier cruzi (glicosomal) ( PDB : 4LSM) [12], Trypanosoma brucei (glicosomal) ( PDB : 4P8R ) [13], Leishmania 3PYM), Homarus americanus ( PDB : 1GPD) [46] and Escherichia coli ( PDB : 1GAD) [47 general, they are similar, with some differences in secondary structure elements; RMSD
557 3rrp - Enhancing the thermostability of fumarase C from Corynebacterium glutamicum via molecular modification 2018 L Lin, Y Wang, M Wu, L Zhu, L Yang, J Lin- Enzyme and microbial, 2018 - Elsevier The modeled structure of cgFumC was completed through homology modeling with the Swiss-Model server by using the crystal structure of the fumarate hydratase Fum ( PDB ID: 3RRP ) from Mycobacterium abscessus as a template, which shares a 75.76% sequence
558 3uam - Computational Studies on Substrate Specificity in Lytic Polysaccharide Monooxygenases 2018 R Arora, RM Yennamalli - 2018 - ir.juit.ac.in 4ALS, 4ALT), Burkholderia pseudomallei CBM33 ( PDB ID: 3UAM ) [10], Bacillus coelicolor CBM2 ( PDB ID: 4OY7), Cellvibrio japonicas CBP33 ( PDB ID: 5FJQ). Page 17. 3 1.5 LPMO and substrate interactions Due to the binding of copper LPMO structure gets stabilized
559 5idv - Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization 2018 I Josts, S Niebling, Y Gao, M Levantino, H Tidow- IUCrJ, 2018 - scripts.iucr.org A total of 30 independent DAMMIF (Franke & Svergun, 2009) runs were performed to generate the initial structure pool (fit not shown). Calculated difference curves between the crystallographic dimer and monomer ( PDB codes 3b60 and 5idv ) show features similar to
560 4j07 - Biomedical Applications of Lumazine Synthase 2018 Y Wei, P Kumar, N Wahome, NJ Mantis- Journal of, 2018 - Elsevier Oligomeric State of LS, Quaternary Structure , Organism, PDB ID 16, 17, 18 Mycobacterium leprae 19 S. cerevisiae 20 Schizosaccharomyces pombe 21, 1DI0 2F59; 2I0F 2OBX 2O6H 2JFB 1C41 2VI5; 2C9B; 2C92; 2C94; 2C97; 2C9D; 1W19; 1W29 4J07 1EJB 1KYV
561 4f82 - Crystal structure of peroxiredoxin 3 from Vibrio vulnificus and its implications for scavenging peroxides and nitric oxide 2018 J Ahn, KK Jang, I Jo, H Nurhasni, GJ Lim, JW Yoo- IUCrJ, 2018 - scripts.iucr.org The structure of reduced Prx3 (C48D/C73S) was determined using the molecular-replacement method with MOLREP in the CCP4 package (Winn et al., 2011) using a putative thioredoxin reductase from Burkholderia ceno- cepacia ( PDB entry 4f82 ; Seattle Structural
562 3hn6 - Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcusaureus 2018 JS Davies, D Coombes, CR Horne, FG Pearce- FEBS, 2018 - Wiley Online Library burgdorferi ( PDB id: 3HN6 )). This is the first time a dimeric oligomeric state for a bacterial NagB has been reported Since there are no representative NagB dimers reported, we constructed two possible dimers of NagB from the E. coli hexamer ( PDB id oligomeric structure
563 5upg - The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical 2018 A Sharma, V Kumar, S Pratap, P Kumar- International journal of biological, 2018 - Elsevier Similarly, a crystal structure of LpxC from P. aeruginosa complexed with the LpxC-4 inhibitors (PDB ID: 5UPG) have also shown the interactions of ligand at these two sites.
564 4f3y 5uy7, 5bq2, 4eqy Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651 2018 Z Nazir, SG Afridi, M Shah, S Shams, A Khan- Microbial pathogenesis, 2018 - Elsevier 2.9. Protein 3D structures prediction. The target proteins structural information is vital for predicting immunogenic domains. The structure information of the target proteins was assessed by BLASTp analysis against Protein Data Bank ( PDB ) [42,43]. 2.10. Antigenicity prediction
565 4qhq - Structural and Functional Characterization of the Escherichia coli MetNI Methionine Transporter 2018 PT Nguyen - 2018 - thesis.library.caltech.edu PTN participated in soaking experiments for the L-semethionine-bound MetNI structure ( PDB :3TUZ) and manuscript preparation. Page 12. xii transporter architecture and mechanism. Science 16. Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J. Crystal structure of a
566 4jcp - Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis 2018 T Martin, YC Lou, CC Chou, SY Wei, S Sadotra- Scientific reports, 2018 - nature.com S1). Like Caenorhabditis elegans Cyp3 (Ccyp3; PDB : 1DYW) and Brugia malayi CypB (BcypB; PDB : 4JCP ), TvCyP1 is a divergent loop cyclophilin and possesses an additional loop in the a) Structure of TvCyP1 dimer showing secondary structural elements ( PDB : 5YB9
567 3krb - Crystal structure of yeast xylose reductase in complex with a novel NADPDTT adduct provides insights into substrate recognition and catalysis 2018 B Paidimuddala, SB Mohapatra, SN Gummadi- The FEBS, 2018 - Wiley Online Library [20, 21] and Giardia lamblia (GlAR; PDB : 3KRB ) homologs [22]. The AKR fold is a namely, hAR bound to D-glyceraldehyde ( PDB : 3V36) and to glucose-6-phosphate ( PDB : 2ACQ) [15, 35] described the enzyme-glyceraldehyde interactions in detail, the structure shows that the
568 3ek1 - A selective determination of the catalytic cysteine pKa of 2cysteine succinic semialdehyde dehydrogenase from Acinetobacter baumannii using burst kinetics and 2018 J Phonbuppha, S Maenpuen- The FEBS, 2018 - Wiley Online Library An AbSSADH homology model was built based on the aldehyde dehydrogenase X-ray structure ( PDB : 3EK1 ) which Based on sequence homology with E. coli GabD for which the structure is known ( PDB :3JZ4), residues Cys75 and
569 3ijp 4f3y, 4ywj 4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae structure and interactions with coenzymes and substrate analog 2018 S Pote, SE Pye, TE Sheahan- Biochemical and, 2018 - Elsevier In case of NgDapB, the position of the coenzyme is modeled using structure of PaDapB ( PDB ID from Bartonella henselae, Burkholderia thailandensis, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Thermotoga maritima ( PDB IDs: 3IJP , 4F3Y, 1ARZ, 4YWJ, 3QY9, 1VM6).
570 5unb - Assessment of hard target modeling in CASP12 reveals an emerging role of alignmentbased contact prediction methods 2018 LA Abriata, GE Tam, B Monastyrskyy- Proteins: Structure, 2018 - Wiley Online Library T0878-D1, 18.30, 12.84, 25.44, 344, 0.85, Burkholderia thailandensis, 5unb Panel E shows the structure of the full target T0912, rainbow-colored to highlight the discontinuities of its Target T0866 ( PDB 5uw2, a homohexamer, Figure 2A) was assessed as 1 evaluation unit of the FM
571 3k2h - Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance 2018 MG Corral, J Haywood, LH Stehl, KA Stubbs- The Plant, 2018 - Wiley Online Library The homology models of A. thaliana DHFR‐TS1 and DHFR‐TS2 were created ab initio based on the structure of the bifunctional DHFR‐TS enzyme from B. bovis (PDB 3K2H; Begley et al., 2011), using the I‐TASSER server (Zhang, 2008).
572 4zju 5ha4, 4zr8 Screening of Potential Lead Molecules Against Prioritized Targets of Multi-Drug Resistant Acinetobacter Baumannii- Insights From Molecular Docking, Molecular Dynamic 2018 S Skariyachan, M Manjunath- Biomolecular Structure, 2018 - Taylor & Francis Fourteen potential drug targets were screened based on their functional role in various biosynthetic pathways and the 3D structures of 9 The study suggests that the aforementioned lead candidates and targets can be used for structure -based drug screening towards MDR A
573 5idv - Conformational States of ABC Transporter MsbA in a Lipid Environment Investigated by Small-Angle Scattering Using Stealth Carrier Nanodiscs 2018 I Josts, J Nitsche, S Maric, HD Mertens, M Moulin- Structure, 2018 - Elsevier are slightly apart, rather than in contact, as seen in the closed structure (Figure 3 2005) and a single MsbA monomer (Figure 4). We imposed several structural restraints, assuming an overall confirmation as observed for P-glycoprotein (Szewczyk et al., 2015) ( PDB : 4Q9H) and
574 3i4e - Three enzymes and one substrate; regulation of flux through the glyoxylate shunt in the opportunistic pathogen, Pseudomonas aeruginosa. 2018 AL Crousilles, SK Dolan, P Brear, DY Chirgadze- bioRxiv, 2018 - biorxiv.org IDH active site architecture with that of ICD in the AceK-ICD complex from E. coli ( PDB ; 3LCB) reveals that X-ray Diffraction, Structure Determination, and Refinement ICL, IDH and ICD were solved using the structural templates 3I4E (to be published), 4ZDA (to be published) and
575 3n58 - Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-l-homocysteine hydrolase from Pseudomonas aeruginosa 2018 J Czyrko, J Sliwiak, B Imiolczyk, Z Gdaniec- Scientific reports, 2018 - nature.com Results. Overall structure of PaSAHase. We present four crystal structures of PaSAHase/ligand/ion(s) complexes at resolutions of 1.35 to 1.75 (Supplementary Information Table S1). Two complexes of Zn 2+ -containing PaSAHase
576 4l82 - Identification of Biological Sulfonamide Degradation 2018 B Ricken - 2018 - d-nb.info 99 4.3. Identification of enzymes responsible for SMX degradation .....103 4.4. Sulfonamides molecule structure influences biodegradability .....105 pdb|4L82| Putative Oxidoreductase Rickettsia felis
577 5eo6 - A molecular, structural, and cellular multiple-level study aimed at understanding the unique reaction catalyzed by the last enzyme in the heme-biosynthesis pathway of 2018 AI Celis Luna - 2018 - scholarworks.montana.edu Overlay of the structures of a representative heme b-bound chlorite dismutase and solvent This research aimed to understand ChdC function at the molecular, structural , and cellular levels The coproheme-bound ChdC structure revealed a helical-loop that is flexible and moves
578 4wny - Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications 2018 AC Vollmer, SJ Bark- Advances in applied microbiology, 2018 - Elsevier Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified t... Universal stress protein 4WNY B. pseudomallei Abendroth, Dranow, Lorimer, and Edwards (2008)
579 3gwc 4emd, 4fkx, 4f4a PROTEIN-LIGAND INTERACTIONS AND STRUCTURE-BASED INHIBITOR DISCOVERY 2018 S Usha, S Selvaraj - 2018 - 14.139.186.108 i) Target structure A target structure experimentally determined through X-ray crystallography or NMR spectroscopy techniques and deposited in the PDB is the ideal starting point for docking. Structural genomics has accelerated the rate at which target structures are
580 4k9d - The glyceraldehyde-3-phosphate dehydrogenase of the shrimp Litopenaeus vannamei: Molecular cloning, characterization and expression during hypoxia 2018 L Camacho-Jimnez, AB Peregrino-Uriarte- Marine Environmental, 2018 - Elsevier We also made a structural analysis in silico of the deduced protein from a comparative the GAPDH holoenzyme from P. versicolor solved by X-ray diffraction (2 ) ( PDB : 1SZJ, chain Finally, the LvGAPDH multimeric complex model was obtained from the former structure with the
581 4whx - The transaminase engineering database (oTAED): a navigation tool in protein sequence and structure space 2018 O Bu, PCF Buchholz, M Grff- Proteins: Structure, 2018 - Wiley Online Library entry 4WHX ) and an amino lyase with activity towards 4-amino-4-deoxychorismate ( PDB entry 2Y4R) [68] as the -TA from Arthrobacter sp. ( PDB entries 5FR9 and 3WWH) which was adapted by John Wiley & Sons, Inc. PROTEINS: Structure , Function, and Bioinformatics
582 3gaf - Sequence and structural studies of proteins associated with cell wall biosynthesis lipolysis and isoniazid drug resistance in Mycobacterium tuberculosis 2018 S Anishetty - 2018 - baadalsg.inflibnet.ac.in Page 4. 63 of recognizing the native structure out of decoy structures 3D coordinates of Isoniazid-NAD adduct ( PDB : 2IDZ) and Triclosan ( PDB : 3OID) was obtained from PDB Rv0547c Oxidoreductase 5e-35 20% FX6-K - Rv0927c Oxidoreductase 1e-32 23% FX6-K 3GAF 41.32
583 4ywj - Coil conversion to strand induced by dimerization 2018 J Laibe, A Caffrey, M Broutin, S Guiglion- Proteins: Structure, 2018 - Wiley Online Library CATH: an expanded resource to predict protein function through structure and sequence -strand interfaces, standard - strand interfaces and domains in CATH (based on PDB release: July 01 interface including a salt bridge between E226-A and H232-B ( 4YWJ ) B. Dimorphic
584 3tmg - The GbsR family of transcriptional regulators: functional characterization of the OpuAR repressor 2018 E Bremer, S Ronzheimer, B Warmbold- Frontiers in, 2018 - frontiersin.org the linker region, an aromatic cage is predicted as the inducer-binding site, whose envisioned architecture resembles that subtilis GbsR protein (Nau-Wagner et al., 2012); it is based on the crystal structure of the DNA-binding protein Mj223 of M. jannaschii ( PDB entry 1KU9
585 5bnt - Structure of aspartate -semialdehyde dehydrogenase from Francisella tularensis 2018 NJ Mank, S Pote, KA Majorek, AK Arnette- Section F: Structural, 2018 - scripts.iucr.org entry 3pzr; Pavlovsky et al., 2012), Pseudomonas aeruginosa ( PDB entry 5bnt ; Seattle Structural N-acetyl- -glutamyl-phosphate reductases (ArgCs), including proteins with known structure : ArgCs from entry 2i3a; Cherney et al., 2007), Salmonella typhi- murium ( PDB entry 2g17
586 4dz4 3dah, 5w15, 3t3w, 3inn, 3hm0, 3ld9, 3l0g, 3tk8, 3swo, 3slg, 3i3f, 4lgo, 5udf, 4ghk, 5kak, 4lgv, 5bq2, 4pca, 4q1t, 5dle Homo Multimer Protein Complexes 2018 P Kangueane, C Nilofer- Protein-Protein and Domain-Domain Interactions, 2018 - Springer 3T3W, 3T94, 3VZD, 3WCM, 3WSG, 3WU4, 4BLP, 4BLQ, 4C01, 4C9S, 4D2E, 4DZ4 , 4FLN, 4FZQ Distribution of homo multimer protein complex structures at the protein data bank ( PDB ) Structure of a homo trimer glycosidase (1AM7) from enterobacteria phage lambda is shown
587 3hzg - Synthse d'analogues nuclotidiques visant l'inhibition de la Thymidylate Synthase Flavine-Dpendante 2018 F Chevrier - 2018 - tel.archives-ouvertes.fr PCF2 : gem-Difluoromthylphosphonate PDB : Protein data bank pH : Potentiel hydrogne 18 Page 20. 19 I. Les bactries : structures et mcanismes d'infection Schma 1 : Structure gnrale d'une bactrie. Cependant, elles possdent des attributs essentiels leur survie
588 5kha 4f4h Kinetics and structural features of dimeric Gln-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites 2018 ARS Santos, ECM Gerhardt, VR Moure- Journal of Biological, 2018 - ASBMB -Proteobacterium Burkholderia thailandensis ( PDB 4F4H) and from the -Proteobacterium Acinetobacter baumannii ( PDB 5KHA ) of dimeric NadE2Gln Given the availability of a 1.7 resolution structure of dimeric NadE2Gln from B. thailandensis ( PDB 4F4H) obtained
589 4lc3 - Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in Streptococcus pneumoniae 2018 X Han, R Sun, T Sandalova, A Achour- Open biology, 2018 - royalsocietypublishing.org The crystal structures of Spr1654 and in complex with PLP and PMP can direct the future rational design of novel therapeutic compounds against S. pneumoniae... The crystal structures were determined by molecular replacement in Phaser [40] using the crystal structure of UDP-4-amino-4-deoxy-l-arabinose-oxoglutarate aminotransferase from Burkholderia cenocepacia (PDB code: 4LC3) as search model.
590 3i4e - Gluconeogenic precursor availability regulates flux through the glyoxylate shunt in Pseudomonas aeruginosa 2018 A Crousilles, SK Dolan, P Brear, DY Chirgadze- Journal of Biological, 2018 - ASBMB domain of each chain (Figure S7), suggesting that catalysis is accompanied by structural rearrangements Comparison of the P. aeruginosa IDH active site architecture with that of ICD in the The structure ( PDB ; 5M2E), solved to 2.7 resolution, was very similar to that reported for
591 4f3p - Local structural motifs in proteins: Detection and characterization of fragments inserted in helices 2018 N Balasco, G Smaldone, A Ruggiero- International journal of, 2018 - Elsevier insertion: A) the substrate binding proteins ( PDB IDs: 1GGG, 1HLS, 1IIT, 2IEE, 2YLN, 4EQ9, 4F3P , 4H5F, 4I62 in red, 3QFH in blue), and C) the elongation factors EF-1A/EF-Tu ( PDB IDs: 1EFC In particular, they could (a) present an irregular loop structure , (b) form -hairpins or
592 4kyx - Contribution of isopentenyl phosphate to plant terpenoid metabolism 2018 LK Henry, ST Thomas, JR Widhalm, JH Lynch- Nature plants, 2018 - nature.com To precisely define the structural basis for substrate selectivities of AtNudx1, we next obtained diffraction-quality crystals for atomic superposition of the previously reported catalytically impaired AtNudx1 mutant, E56A, with GPP bound ( pdb 5GP0) and our structure with IPP
593 4zju - Structure and substrate specificity of ketoacylacyl carrier protein synthase III from Acinetobacter baumannii 2018 WC Lee, MC Jeong, Y Lee, C Kwak- Molecular, 2018 - Wiley Online Library detailed structures of FAS-related proteins from A. baumannii are still lacking except for the unpublished structure of FabI ( PDB ID: 4ZJU ). To our knowledge, the AbKAS III structures KAS III orthologs, whereas only one is found in the A. baumannii genome. Our structure and
594 3r9r 3lp8, 5vev Studying the mechanism and action of Purine biosynthesis enzymes in Mycobacterium Tuberculosis H37RV 2018 SJ Almehmadi - 2018 - lra.le.ac.uk Structural determination of SAICARs in M. tuberculosis and refinement, results tetraacetic acid F1 forward primer Fc calculated structure factors Fo observed structure factors Fo-Fc OD optical density ORF open reading frame PCR polymerase chain reaction PDB protein Data
595 5udf - Translocation of lipoproteins to the surface of gram negative bacteria 2018 Y Hooda, TF Moraes- Current opinion in structural biology, 2018 - Elsevier The model of LolCDE was obtained from the structure of LptBFG ( PDB ID: 5UDF )and is The structure of type IVa pilus machinery from Myxococcus xanthus ( PDB ID: 3JC9) was used as In contrast, Slam possesses a unique domain architecture and no structure of any protein of
596 2kn9 - A two-headed monster to avert disaster: HBS1/SKI7 is alternatively spliced to build eukaryotic RNA surveillance complexes 2018 JO Brunkard, B Baker- Frontiers in plant science, 2018 - frontiersin.org Recently, structural studies of the cytoplasmic RNA exosome in yeast and humans have revealed the crucial importance of SKI7 in bridging ... The N-terminus of SKI7 (through the patch 4-like motif) structure was modeled by Phyre24, which used structures of YY1-associated factor 2 (PDB 2D9G), HBV-associated factor (PDB 2CRC), Rubredoxin B (PDB 2KN9), NEMO CoZi (PDB 4OWF), and TAB3-NZF (PDB 3A9K).
597 3ej2 - Synthesis and Activity of 1, 2, 3-Triazolyl-chalcones Against the Fungus Colletotrichum lindemuthianum 2018 JC Pessoa, RF Azevedo, SF Mota- Letters in Organic, 2018 - ingentaconnect.com 3.6. Enzymes Complexed with Ligands Similar to Com- pound 1a The structure of compound 1a proteins were downloaded from the RCSB Protein Data Bank (http://www. pdb .org) [36 protein kinase (STPK; code: 2AYP) [29], inorganic phosphatase (IP; code: 3EJ2 ) [30], Bruton's
598 5upg - Widening the Therapeutic Window: Time-Dependent Inhibitors of LpxC and InhA for Treating Multidrug-Resistant Bacterial Infections 2018 C Gu - 2018 - search.proquest.com 46 Figure 2.10. X-ray crystal structure of paLpxC in complex with PF5081090 ( 5UPG . pdb ). ... 48 PD Pharmacodynamics PDB Protein Data Bank PIPES Piperazine-N,N-bis(2-ethanesulfonic acid) Sfp Phosphopantetheinyl transferase SKR Structure -kinetic relationship
599 4egq - Identification of natural inhibitors against Acinetobacter baumanniid-alanine-d-alanine ligase enzyme: A multi-spectrum in silico approach 2018 S Ahmad, S Raza, SW Abbasi, SS Azam- Journal of Molecular Liquids, 2018 - Elsevier The protein after retrieval from PDB was subjected to a preparation phase, where only one 5), with minor effect on the overall structure baumannii), (3V4Z, Yersinia pestis), (4DGJ, Burkholderia xenovorans), (4EGO, Burkholderia ambifaria), ( 4EGQ , Burkholderia pseudomallei)
600 4ot8 - Chloroplastic serine hydroxymethyltransferase from Medicago truncatula: a structural characterization 2018 M Ruszkowski, B Sekula, A Ruszkowska- Frontiers in plant, 2018 - ncbi.nlm.nih.gov It is very intriguing to see that, to our best knowledge, the conformation of the γ-hydroxyl group of PLP-Ser external aldimine is unique in comparison with nearly all other SHMT complexes in the PDB (PDB IDs: 1kkp, 1yjy, 2via, 2vmp, 2vmt, 2vmw, 2w7f, 2w7k, 4ot8), except for the alternative conformation (30% occupancy) in the E53Q mutant of Geobacillus
601 5ify - A structural and functional perspective on the enzymes of Mycobacterium tuberculosis involved in the L-rhamnose biosynthesis pathway 2018 DK Dhaked, MB Divya, L Guruprasad- Progress in Biophysics and, 2018 - Elsevier Some representative crystal structures of RmlA-D were retrieved from PDB and were compared with the models constructed The structure superposition of some known RmlAs (PDB_IDs: 1FXO, 1IIM, 1H5T, 3PKP, 5IFY and 6B5E) revealed their highly similar structures
602 2lgo - A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures 2018 J Zhou, AE Panaitiu, G Grigoryan- bioRxiv, 2018 - biorxiv.org decompose the target structure to be designed into structural building blocks we call TERMs (tertiary motifs) and use rapid structure search against the Protein Data Bank ( PDB ) to identify sequence patterns associated with each TERM from known protein structures that contain it
603 3qxz 3qre, 3qk8, 3swx, 4qtp, 3oc7 Similarity/dissimilarity analysis of protein structures based on Markov random fields 2018 J Wu, T Zhou, J Tao, Y Hai, F Ye, X Liu, Q Dai- Computational biology and, 2018 - Elsevier Recently, the growth of the Protein Data Bank ( PDB ) (Berman et al., 2000) has been accelerated by a large scale As a result, fast and efficient algorithms for protein structure comparison have become more important to take advantage of the huge amount of structural data
604 4odj - A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs) 2018 C Ehrt, T Brinkjost, O Koch- PLoS computational biology, 2018 - journals.plos.org In parallel with the ever increasing number of available protein structures in the Protein Data Bank ( PDB )[1], various in silico techniques were developed to apply this structural knowledge[2]. In addition to molecular docking, structure -based pharmacophore searches, and
605 5bq2 - Molecular modelling and dynamic simulation of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) from Mycobacterium tuberculosis using in silico 2018 MA Isa, RS Majumdar, S Haider- Informatics in Medicine, 2018 - Elsevier structure of UDP-N-acetylglucosamine -1-carboxyvinyltransferase (MurA) is not available in PDB . Therefore, the 3D structure was determined through the sequence, obtained from NCBI (Accession result of a BLASTp search against PBD, six proteins (3SG1, 5BQ2 , 3ISS, 1A2N
606 5ifz - SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for 2018 JM Dana, A Gutmanas, N Tyagi, G Qi- Nucleic acids, 2018 - academic.oup.com 5.3.1.34 D-erythrulose 4-phosphate isomerase Q9ZB26 99% 5ifz 5.3.1.6 Ribose-5 of the protein sequence space 40-fold, expanding the applicability of structure -based an positions from Ensembl enables a more direct cross-referencing of genomic data from PDB structures
607 4wkw - Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis 2018 A Negri, P Javidnia, R Mu, X Zhang- ACS infectious, 2018 - ACS Publications Compared with published crystal structures of Rv2466c (PDB ID: 4NXI, 4ZIL) and the M. leprae homologue (PDB ID: 4WKW), there were significant conformational changes in one subunit of our structure
608 3kc6 3khw Structure and Function of Influenza Virus Ribonucleoprotein 2018 CY Lo, YS Tang, PC Shaw- Virus Protein and Nucleoprotein Complexes, 2018 - Springer These structures include PDB : 2VY7, 2VY8, 3KC6 , 3KHW, 2GMO (solution structure of NLS-domain). Structures composing of both domains are also available ( PDB : 2VY6, 3CW4) (Tarendeau et al. 2007; Tarendeau et al. 2008; Kuzuhara et al. 2009; Yamada et al
609 4ege - Trichomonas vaginalis metalloproteinase TvMP50 is a monomeric Aminopeptidase P-like enzyme 2018 R Arreola, JL Villalpando, J Puente-Rivera- Molecular, 2018 - Springer Superposition with E. coli Prolidase Structure ( PDB : 4QR8) 4EGE and 4QR8 are dimers but 4EGE contains a CRE_N domain in the N-terminal determined N-terminal domain; however, as we showed in this study, this domain maintains a closely related architecture with AMP_N
610 4tyz - PROTEIN-PROTEIN INTERACTIONS OF HUMAN PARVOVIRUS B19 NS1 AND IDENTIFICATION OF THE NS1 TRANSCRIPTIONAL TRANSACTIVATION DOMAIN 2018 AL Morano - 2018 - repository.arizona.edu Page 1. PROTEIN-PROTEIN INTERACTIONS OF HUMAN PARVOVIRUS B19 NS1 AND IDENTIFICATION OF THE NS1 TRANSCRIPTIONAL TRANSACTIVATION DOMAIN Structure: Residues 112-214 share 32% sequence identity to x-ray crysal structure in PDB file 4TYZ chain A (a protein of unknown function).
611 4ywj 3ijp, 4f3y Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly 2018 SAJ Watkin, JR Keown, E Richards- Biochemical, 2018 - portlandpress.com DHDPR from a total of nine bacterial species, whereas no plant DHDPR structures were previously and X-ray crystallography to demonstrate how small elements of secondary structure are able Additionally, we use kinetic assays and an analysis of the structural flexibility of the
612 5unb - NEPRE: a Scoring Function for Protein Structures based on Neighbourhood Preference 2018 S Liu, X Xiang- bioRxiv, 2018 - biorxiv.org Based on the testing results and the comparison with several other structure assessment methods, we report that the neighborhood structural correctness. MATERIALS AND METHODS composed of 14,647 PDB structures , which were selected from the NCBI VAST (the vector
613 4j07 - Strategies to improve the immunogenicity of subunit vaccine candidates 2018 Y Wei - 2018 - kuscholarworks.ku.edu Oligomeric state of lumazine synthase Quaternary structure Organism PDB ID Pentamer 1DI0 2F59 ; 2I0F 2OBX 2O6H 2JFB 1C41 2VI5; 2C9B; 2C92; 2C94; 2C97; 2C9D; 1W19; 1W29 4J07 1EJB 1KYV; 1KYX; 1KYY Decamer Brucella spp
614 3r4t 4ffc Novel-Substituted Heterocyclic GABA Analogues. Enzymatic Activity against the GABA-AT Enzyme from Pseudomonas fluorescens and in Silico Molecular Modeling 2018 E Tovar-Gudio, J Guevara-Salazar, J Bahena-Herrera- Molecules, 2018 - mdpi.com molecular docking studies to explain their inhibitory character based in different structural and electronic to the concept of molecular similarity, which states that molecules with similar structure will have Figure 6 shows the cavity of the GABA-AT ( PDB : 1SF2 from Escherichia coli
615 5vmt 3hja Crystal structure of GAPDH of Streptococcus agalactiae and characterization of its interaction with extracellular matrix molecules 2018 R Nagarajan, S Sankar, K Ponnuraj- Microbial pathogenesis, 2018 - Elsevier S1). The protein BLAST against Protein Data Bank ( PDB ) led to 97 hits with recently determined 71% and 69% sequence identity with S. pneumoniae (5M6D), Nessiera gonorrhea ( 5VMT ) and S to mixed-holo structure (highest resolution of 1.36 ), the present structure (Apo, 2.6
616 3kw3 - Computational evidence of a new allosteric communication pathway between active sites and putative regulatory sites in the alanine racemase of Mycobacterium 2018 J Jyothikumar, S Chandani, R Tangirala- bioRxiv, 2018 - biorxiv.org Fig 3 Structure -based multiple sequence alignment of alanine racemases E. coli ( PDB code: 2RJG), S. pneumoniae ( PDB code: 3S46), P. fluorescens ( PDB code: 2ODO), P. aeruginosa ( PDB code: 1RCQ), A. baumannii ( PDB code: 4QHR), B. henselae ( PDB code: 3KW3 )
617 3men - Design of Drugs by Filtering Through ADMET, Physicochemical and Ligand-Target Flexibility Properties 2018 M Martnez-Archundia, M Bello, J Correa-Basurto- Rational Drug Design, 2018 - Springer the three-dimensional model of the human HDAC6, considering some of the crystal structures available for this protein, which maintained some structural identities (2VCG (37%), 1ZZ0 (37%), 1C3P (29%), 3MEN (36%), 3COY 4. Finally, the crystal structure of PDB : 3F07 was
618 3mqw 3m1x Identification of a perchloric acid-soluble protein (PSP)-like ribonuclease from Trichomonas vaginalis 2018 A Villalobos-Osnaya, G Garza-Ramos, IN Serratos- Parasitology, 2018 - Springer The trimeric model was built using a crystal- lographic ribonuclease structure ( PDB ID: 3R0P) as a tem resolution less than 2 (1QU9, 3M1X, 2UYK, 2UYN, 2CVL, 1JD1, 1QD9, 3QUW, 3MQW , 3VCZ, 1ONI 4e). To gain insight the secondary structure properties of rTv-PSP1, itsfar
619 3l56 - Evolutionary targeted discovery of influenza A virus replication inhibitors 2018 H Patel - 2018 - uhra.herts.ac.uk 4.4.2 Structure and predicted binding site locations of the NEP NCI National cancer institute NEP Nuclear export protein NLS Nuclear localisation signal NS1 Non- structural protein 1 basic protein 1 PB2 Polymerase basic protein 2 PBS Phosphate buffer saline PDB Protein data
620 6blj - Acceptor Stem Differences Contribute to Species-Specific Use of Yeast and Human tRNASer 2018 MD Berg, J Genereaux, Y Zhu, S Mian, GB Gloor- Genes, 2018 - mdpi.com sapiens (4L87; [46]), Naegleria fowleri ( 6BLJ ), and Thermus thermophilus (1SET; [47]) from the Protein Data Bank were used to construct a structural alignment. ASN.1 files for each structure were obtained from the Molecular Modeling Database, and the structures were aligned
621 3gvh - Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase 2018 JM Gonzlez, R Marti-Arbona, JCH Chen- Section F: Structural, 2018 - scripts.iucr.org Data-collection and quality statistics are summarized in Table 3. 2.6. Structure solution and refinement The malate/lactate dehydrogenase from Brucella melitensis ( PDB entry 3gvh ; Seattle Structural Genomics Center for Infectious Disease, unpublished
622 4o5o - Engineering Erg10 Thiolase from Saccharomyces cerevisiae as a Synthetic Toolkit for the Production of Branched-Chain Alcohols 2018 P Torres-Salas, V Bernal, F Lopez-Gallego- Biochemistry, 2018 - ACS Publications Using a combined computational/experimental approach, and guided by structural information, we have studied the potential of thiolases to with novel properties, the naturally occurring metabolism of microorganisms is not always sufficient to obtain any desired structure
623 3oks - YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations 2018 H Land, MS Humble- Protein Engineering, 2018 - Springer File > Load > yob file from Your working directory. File > Load > Pdb file from internet. To align the structures [31] 1.531. 386 g. 29.8. 3OKS h. 1.702. 717. 27.8 g Monomer. h Crystal structure (444 residues) of a 4-aminobutyrate transaminase from Mycobacterium smegmatis [34]
624 4i1i 4h7p Anlise de aspectos estruturais em imunoinformtica utilizando candidatos vacinais contra Leishmaniose que foram selecionados usando vacinologia reversa. 2018 JPL Velloso - 2018 - arca.fiocruz.br Considering the importance of protein structure in immunological interactions and in vaccine infantum, protein modeling, molecular docking, structural protein disorder. Page 11. LISTA DE QUADROS NCBI - National Center for Biotechnology Information PDB - Protein Data Bank
625 5vn4 - Crystal structures of APRT from Francisella tularensis an NHN hydrogen bond imparts adenine specificity in adenine phosporibosyltransferases 2018 GC Pavithra, UA Ramagopal- The FEBS journal, 2018 - Wiley Online Library [2]. The structure along with core PRPP binding domain also possesses a catalytic loop It should be noted that the overall architecture of FtAPRT is very similar to that of other canonical APRTs ( PDB -1QB7) [4] and Trypanosoma brucei ( PDB - 5VN4 ) with a C-terminal extension
626 4odj - CrossStrand Disulfides in the Hydrogen Bonding Site of Antiparallel sheet (aCSDhs): Forbidden Disulfides that are Highly Strained, Easily Broken 2018 NL Haworth, MJ Wouters, MO Hunter, L Ma- Protein, 2018 - Wiley Online Library Examples include interleukin 36 receptor antagonist (PDB: 1md6) and the previously mentioned ML domains. Other aCSDhs span only short segments of sequence straddling a β‐hairpin (PDBs: 5bvw, 3fl7, 1htd, 3ngm, 4odj).
627 6bfu - Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis 2018 RN Kirchdoerfer, N Wang, J Pallesen, D Wrapp- Scientific reports, 2018 - nature.com Structural description of SARS-CoV S 2P ectodomain Structure of the SARS-CoV S 2P ectotodomain fusion peptide 24 adopts a conformation distinct from equivalent regions in (b) alpha- (HuCoV-NL63, 5SZS. pdb 20 ) and (c) deltacoronavirus spikes (PDCV S, 6BFU . pdb 21 ) as
628 3tf6 - DLSCORE: A Deep Learning Model for Predicting Protein-Ligand Binding Affinities 2018 M Hassan, DC Mogollon, O Fuentes, S Sirimulla - 2018 - .s3.amazonaws.com In designing DLSCORE architecture , we divided the entire method into two parts 2 PDB IDs 4rqv, 4tkb, 1met, 5c5t, 3p8p, 2iuz, 4kfq, 3ifl, 4p6c, 1oyt, 4ibg, 3uri, 3t01, 1o5e, 3qgy, 3kgu, 2h21, 3agl, 3n7a, 1qkt, 1o2j, 1azm, 1afk, 1g54, 3nu3, 2yhw, 4mme, 2f94, 3vha, 3tf6 , 2pvj, 1fkb
629 3lgj 3pgz Modified enzymes 2018 AJ Heron, RV Bowen, M Bruce- US Patent App. 15, 2018 - Google Patents In order to assess whether a suitable protein structure exists to use as a template to build a protein model, a search is performed on the protein data bank ( PDB ) database The sequence alignment and template structure are then used to produce a structural model of the The polynucleotide binding motif may be selected from any of those shown in Table 5 below. Bartonella 3LGJ, Q6G302 homo-tetramer
630 4gnv - Structural and mechanistic analysis of a -glycoside phosphorylase identified by screening a metagenomic library 2018 SS Macdonald, A Patel, VLC Larmour- Journal of Biological, 2018 - ASBMB in BglP it is a glutamine, as seen in the structural overlay of Figure 8C wherein the 2FGlc- BglP structure is superimposed on the structures of two other GH3 -N-acetylglucosaminidases (NagZ from Burkholderia cenocepacia in complex with GlcNAc [ PDB : 4GNV ] and NagZ from
631 5umh 5vxt Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch 2018 CR Schlachter, L Daneshian, J Amaya- Insect biochemistry and, 2018 - Elsevier Here, we have determined the spectroscopic, structural and metabolic properties of TuIDRCD, the first arthropod ID-RCD used for determination, refinement, and validation of mTuIDRCD structure ; however, in this case the structure of mbp-(t48)TuIDRCD ( PDB code: 5VG2
632 3nfw 4l82 Crystal structure of the flavin reductase of Acinetobacter baumannii p-hydroxyphenylacetate 3-hydroxylase (HPAH) and identification of amino acid residues 2018 A Yuenyao, N Petchyam, N Kamonsutthipaijit- Archives of Biochemistry, 2018 - Elsevier The structure was refined to 2.9 resolution with an R work and R free of 0.2534 and 0.2889, respectively somnus ( PDB ID: 2R0X, Z = 21.8 RMSD = 1.3 ), Mycobacterium thermoresistibile nitrilotriacetate monooxygenase component B (NTA-MoB) ( PDB ID: 3NFW , Z = 21.5
633 3sbx - Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales 2018 S Siddaramappa, V Viswanathan- Microbial, 2018 - ncbi.nlm.nih.gov using blastp analysis and acquired from GenBank, rast or the Protein Data Bank ( PDB ) http://espript.ibcp.fr/ESPript/ESPript/) to depict similarities and secondary structure information In this context, the structural and functional similarities between different CrtI homologues need
634 3pgz 5j3b Caracterizao molecular da atividade de interao da protena RPA-1 com os telmeros de Leishmania spp. 2018 GAGD Santos - 2018 - repositorio.unesp.br Recently, using molecular dynamics simulations we have shown that the tertiary structure of LaRPA-1 differs from human and yeast RPA-1 and A structural search for proteins that share with the TEP domains of protein-DNA interaction, showed that in the genome of Leishmania
635 3rih 3pk0 Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis 2018 E Mallette, MS Kimber- Biochemistry, 2018 - ACS Publications We determined the structure of APDH in both apo form (at 1.7 ) and as a ternary enzyme complex with NADP + and aminoacetone... This work has shown that 3PK0 (APDHMSM0779) is an orthologue, and analysis (see below) suggests that 3RIH is also likely a Mycobacterial APDH orthologue
636 3qxz 3s6o, 3i3f Analysis of Pseudo-Symmetry in Protein Homo-Oligomers 2018 CJR Rajendran - 2018 - scholarworks.iupui.edu Figure 3.2: PDB File format In a PDB file, as mentioned in the above figure 3.2, the Atom type is used to capture the structures are calculated to get the overall structural index Structure Index for Trimers can be calculated by measuring the distance between the original
637 4ffc 3r4t Novel-Substituted Heterocyclic GABA Analogues. Enzymatic Activity against the GABA-AT Enzyme from Pseudomonas fluorescens and In Silico Molecular 2018 E Tovar-Gudio, JA Guevara-Salazar- Molecules, 2018 - mdpi.com -Aminobutyric acid (GABA) is the most important inhibitory neurotransmitter in the central nervous system, and a deficiency of GABA is associated with serious neurological disorders. Due to its low lipophilicity, there has been an intensive search for new molecules with increased
638 4k73 - L, D-transpeptidases de Mycobacterium tuberculosis: estudo das interaes com antibiticos -lactmicos e triagem de fragmentos 2018 GA Libreros-Ziga - 2018 - repositorio.unesp.br structure of LdtMt3 and its interactions with -lactam antibiotics, as well as the PDB Banco de dados de protenas (Protein Data Bank) Structural basis for the interaction and processing of -lactam antibiotics by L,D- transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis
639 3o0h - Sulphur (lone pair) interactions with FAD in flavoenzymes 2018 RFN Silva, ACS Sacco, I Caracelli- Zeitschrift fur, 2018 - eprints.sunway.edu.my Finally, in the 22 SOX enzymes found in PDB , there were 45 monomers having FAD S(lp)(FAD) interactions in three examples of GR enzymes: (a) 1K4Q [64], (b) 3O0H [64] and with FAD via S(lp)(FAD) interactions that pro- vide stability to the secondary structure and
640 4wi1 - Drug targeting of one or more aminoacyl-tRNA synthetase in the malaria parasite Plasmodium 2018 Y Manickam, R Chaturvedi, P Babbar- Drug Discovery, 2018 - csmres.co.uk site of Pf-LRScyto effectively and the crystal structure for the editing domain of enzymes with this scaffold is known different inhibitor molecules: halofuginone (HF, yellow PDB ID: 4YDQ), glyburide (violet, PDB ID: 5IFU), TCMDC-124506 (orange, PDB ID: 4WI1 ) and modeled
641 2khp - NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY IN THE STUDY OF PROTEIN-LIGAND INTERACTIONS 2018 DL Morris - 2018 - rave.ohiolink.edu Structures of target proteins were obtained from the Protein Data Bank (PDB). The PBD code for BrmGRX is 2KHP and hGRX1 is 1JHB.
642 3gtd 3rd8, 3tv2 Mapeamento das bases estruturais e suas correlaes com patogenias humanas associadas mutaes na fumarase humana 2018 MAA Aleixo - 2018 - teses.usp.br HsFH crystal structure was solved at 1.8 resolution and identified HEPES molecules complexed with the FumC (1YFE);Saccharomyces cerevisiae (strain ATCC 204508 / S288c) FH (1YFM); Rickettsia prowazekii FH ( 3GTD ), Mycobacterium tuberculosis PDB Protein Data Bank
643 3ijp - Crystal structure of dihydrodipicolinate reductase (Pa DHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor 2018 CW Lee, SH Park, SG Lee, HH Park, HJ Kim, HJ Park- Scientific reports, 2018 - nature.com EcDHDPR; UniProtKB: P04036; PDB : 1DRU), B. henselae (BhDHDPR; UniProtKB: Q6G2G3; PDB : 3IJP ), A. variabilis P40110; PDB : 5EER), and M. tuberculosis (MtDHDPR; UniProtKB: P9WP23; PDB : 1YL5 The crystal structure of DPA-bound PaDHDPR was also obtained in the
644 4dlp 4ncx Aminoacyl tRNA Synthetases as Malarial Drug Targets: A Comparative Bioinformatics Study 2018 DW Nyamai, OT Bishop- bioRxiv, 2018 - biorxiv.org are highly conserved in their catalytic domains, in general aaRSs show sequence, structural 62 catalytic site architecture and the manner of charging tRNA [18,20] the connective peptide I (CPI) in all enzymes in this class whose structure is characteristic of 113
645 5woq - In-Silico Structural & Molecular Characterization Of Clgr From Mycobacterium Tuberculosis 2018 YN Joshi, RD Salunkhe - ijiset.com was obtained through SWISS MODEL server using resolution 1.8 A structure of ClgR from Mycobacterium smegmatis ( PDB Id: 5woq .2.A K, Bordoli L, Kopp J, Schwede T. The SWISSMODEL Workspace: A web-based environment for protein structure homology modelling
646 4g6c 3laa Blind prediction of protein B-factor and flexibility 2018 D Bramer, GW Wei- The Journal of chemical physics, 2018 - aip.scitation.org MENU. SIGN IN. Sign in/Register. Enter words / phrases / DOI / ISBN / authors / keywords / etc. SEARCH; CITATION SEARCH; ADVANCED SEARCH. Search in: This Publication. search. Advanced
647 3meq - Activity-related microsecond dynamics revealed by temperature-jump Forster resonance energy transfer measurements on thermophilic alcohol dehydrogenase 2018 MB Vaughn, J Zhang, TG Spiro, RB Dyer- Journal of the, 2018 - ACS Publications Previous studies of a thermophilic alcohol dehydrogenase (ht-ADH) demonstrated a range of discontinuous transitions at 30 C that include catalysis, kinetic isotope effects, protein hydrogendeuter... Figure 1. Structure of ht-ADH in green with NADH and alcohol in cyan. The three tryptophan residues are yellow. This structure was created from an overlap of PDB: 1RJW and 3MEQ
648 5dld 4hwg The tetrameric structure of sialic-acid-synthesizing UDP-GlcNAc 2-epimerase from Acinetobacter baumannii: a comparative study with human GNE 2018 TP Ko, SJ Lai, TJ Hsieh, CS Yang, Y Chen- Journal of Biological Chemistry, 2018 - ASBMB Crystal structures of the non-hydrolyzing enzyme are known for at least ten species [ PDB ID: 1F6D, 1O6C, 1V4V, 3BEO, 3DZC, 3OT5, 4HWG, 4NEQ, 5DLD , 5ENZ, and The UDP-interactions with NeuC are fewer than those observed in the GNE structure , probably because
649 3o0m - Characterization of Mycobacterial Flap Endonuclease FenA and RNA Helicase HelY 2018 MLL Uson - 2018 - search.proquest.com There, she focused on the detection of circulating tumor cells and structural characterization of EphA3, a 122 Figure 4.3 Manganese ions in the FenA active site ..... 126 Figure 4.4 Active site architecture and structure -guided mutagenesis
650 4qhq - Dveloppement d'un alphabet structural intgrant la flexibilit des structures protiques 2018 I Sekhi - 2018 - tel.archives-ouvertes.fr 84 4.2.2 Architecture du site web 2.5 Comparaison de temps d'excution de SAFlex- PDB avant et aprs optimisation ensemble de conformations gomtriques reprsentatif des fragments protiques, appels lettres structurales (LS) , et destines simplifier la structure 3D d
651 4whx - ω-Transaminases as Promising Biocatalysts for the Chiral Synthesis of β-Amino Acids 2018 MSO Buss - thesis The -Transaminase Engineering Database (oTAED): a navigation tool in protein sequence and structure space o Review about the protein stability engineering in silico tool FoldX ... The largest homologous family (HFam 11) includes 90% of all Fold type IV sequences and 23 annotated structures such as a branched-chain-amino-acid TA (PDB entry 4WHX)
652 5ts2 - Umbrella Sampling and X-ray Crystallographic Analysis Unveil an Arg-Asp Gate Facilitating Inhibitor Binding Inside Phosphopantetheine Adenylyltransferase 2018 A Mondal, R Chatterjee, S Datta- The Journal of Physical, 2018 - ACS Publications In this study, we have attempted to further comprehend the structural details and mechanisms involved in AcCoA binding Material and method: MD simulations The PPATWT-AcCoA structure used for this study was obtained from RCSB- PDB ( PDB ID: 3X1J)
653 3rih 3uve The Role of Charged Residues in the Structural Adaptation of Short-Chain Alcohol Dehydrogenase (SDR) from Thermophilic Organisms to High Temperatures 2018 Bulletin of Moscow University. Series 2. Chemistry, 2018 - cyberleninka.ru PDB (*), 3RIH (Mycobacterium Abscessus*) 2,36 2,36 1,32 7,62 8 THE ROLE OF CHARGED RESIDUES IN THE STRUCTURAL ADAPTATION OF SHORT-CHAIN
654 4w65 - Isolation of -1, 3-Glucanase-Producing Microorganisms from Poria cocos Cultivation Soil via Molecular Biology 2018 Q Wu, X Dou, Q Wang, Z Guan, Y Cai, X Liao- Molecules, 2018 - mdpi.com The glycoside hydrolase -1,3-glucanase, extensively distributed among plants, fungi, and bacteria, acts on 1,3--glucosidic bonds of structural -1,3-glucans to hydrolyze or transfer glycosides [1,2]. Based on the hydrolysis position, -1,3-glucanases are divided into endo-type
655 3tde 3rv2, 3s82 Synthesis of non-natural cofactor analogs of S-adenosyl-L-methionine using methionine adenosyltransferase 2018 J Thorson, T Huber, J Zhang, S Singh- US Patent 9,879,043, 2018 - freepatentsonline.com marinum ( PDB code 3RV2), Mycobacterium avium ( PDB code 3S82), Mycobacterium tuberculosis ( PDB code 3TDE ), Rattus norvegicus [36 Protein Data Bank ( PDB ) ID:1RG9), hMAT2A ( PDB ID:2PO2) and hMAT1A ( PDB ID:2OBV) on the hMAT2A homodimeric structure
656 4ix8 - Comprehensive genomic analysis of the TYROSINE AMINOTRANSFERASE (TAT) genes in apple (Malus domestica) allows the identification of MdTAT2 conferring 2018 H Wang, Q Dong, D Duan, S Zhao, M Li- Plant Physiology and, 2018 - Elsevier sequence identity for residues 44423), whereas MdTAT3 structure most closely matched that of Leishmania infantum TAT ( PDB ID: 4IX8 .A; RMSD To better understand the gene structure diversity of apple TAT proteins, the intron-exon organization in the coding sequences of
657 4eo9 - Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE 2018 DJ Rigden, JMH Thomas, F Simkovic- Section D: Structural, 2018 - scripts.iucr.org 1e59) was determined at a very high resolution (1.3 A ) while the other ( PDB entry 4eo9 ) was only at moderate resolution (2.45A). From this set, the structure of ecdysone phosphate phosphatase ( PDB entry 3c7t The third was a set of manually edited crystal structure derivatives
658 5unb - Universal architectural concepts underlying protein folding patterns 2018 A Lesk, R Subramanian, L Allison, D Abramson- bioRxiv, 2018 - biorxiv.org to give proteins their intricate three-dimensional shapes and folding patterns (tertiary structure ) Unravelling protein architecture and discovering the relationship among these three major levels of of protein folding patterns have revealed recurrent themes at all structural levels (2
659 5kak - Protein-protein and domain-domain interactions 2018 P Kangueane, C Nilofer - 2018 - books.google.com 1.10) structures It is important to under- stand the physical and chemical features of amino acids to understand protein folding, structure , function, and 1.4 A covalent bond is illustrated using cysteine with corresponding bond length 1.5 Structural Motifs Proteins are made of
660 3grk 3s55, 4eit, 3tzq, 4j07 Crosslinked helix dimers as versatile scaffolds for mimicking topologically complex epitopes 2018 MG Wuo - 2018 - search.proquest.com 1 1.2 Surface architecture variation among PPIs affect ligandability ..... 3 aliphatic core but lacks any heptad repeat structure and knob/hole packing orientation. ( PDB Codes: 1LLM, 1TMX, 3V3E) .... 57
661 3qxz - Purification, crystallization and X-ray crystallographic analysis of enoyl-CoA hydratase/isomerase-family protein from Cupriavidus necator H16 2018 H Seo, KJ Kim- Biodesign, 2018 - bdjn.org The structure of H16_B0756 was determined by molecular replacement with the CCP4 version of MOLREP (Vagin and Teplyakov 2009) using the structure of probable enoyl-CoA hydratase/isomerase from Mycobacterium abscessus ( PDB code 3QXZ ) as a search model
662 2lwk - RNA on the move: the plasmodesmata perspective 2018 BC Reagan, EE Ganusov, JC Fernandez, TN McCray- Plant Science, 2018 - Elsevier While this synthetic RNA consists of only 32 nucleotides, it has a corresponding radius of gyration of 15.48 Å (1.548 nm) when bound to the small molecule DPQ (6,7-dimethoxy-2-(piperazin-1-yl)quinazolin-4-amine) (PDB ID: 2LWK)
663 4z9n - Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis 2018 K Keidel, F Amman, I Bibova, J Drzmisek, V Benes- RNA, 2018 - rnajournal.cshlp.org Besides its role in the stabilization of the RNA duplexes, Hfq can also actively remodel the structure of RNAs and increase or decrease the stability of BLAST search unveiled that the BP3831 protein exhibits high homology with the entry 4Z9N in the PDB protein database
664 6c87 6byq SIMBAD: a sequence-independent molecular-replacement pipeline 2018 AJ Simpkin, F Simkovic, JMH Thomas- Section D: Structural, 2018 - scripts.iucr.org researchers involved. All cases involve the crystallization of a known contaminant. Examples involving the use of SIMBAD for novel structure solution are available elsewhere, such as PDB entries 6byq, 6c87 and 5wol. Cases illustrating
665 3oa3 3ngj, 3ndo Methods And Microorganisms For The Production Of 1, 3-Butanediol 2018 R Mahadevan, A Yakunin, P Gawand- US Patent App. 15, 2018 - Google Patents 2.4.). In some embodiments, DERA enzymes can be described as class I aldolases that form covalent Schiff base intermediates. In all studied structures , DERA adopts the classical eight-bladed TIM barrel fold. The oligomerisation
666 6cau - Phase determination of the UDP-N-acetylmuramic acid: L-alanine ligase (MurC) crystal from Mycobacterium bovis 2018 PW Seo, JS Kim - 2018 - bdjn.org Haemophilus influenzae ( PDB ID 1P31, 1GQQ), Acinetobacter baumannii ( PDB ID 6CAU ), Yersinia pestis ( PDB ID 4HV4 of the PHENIX suite (Adams et al., 2010) using Y. pestis MurC ( PDB ID 4HV4 Structure of Escherichia coli UDP-N-acetylmuramoyl: L-alanine ligase (MurC)
667 5unb - Supplementary materials to PconsC4: fast, free, easy, and accurate contact predictions. 2018 M Michel, D Menndez-Hurtado, A Elofsson - 2018 - pdfs.semanticscholar.org PconsC4 is trained on a set of 2759 proteins culled from PDB using PISCES (Wang and in (Michel et al., 2017) and the 46 proteins from CASP12 with available structures , Table S6 It is pre-trained to predict secondary structure and surface accessibility for each residue (golden
668 3rih 3uve The Role of Charged Residues in the Structural Adaptation of Short-Chain Alcohol Dehydrogenase (SDR) from Thermophilic Organisms to High Temperatures 2018 AV Popinako, MY Antonov, EY Bezsudnova- Moscow University, 2018 - Springer Protein structures from PDB database are marked with asterisk 3RIH (Mycobacterium Abscessus tion involving specific patterns of the distribution of dif- ferent residues in the structure , including their distribu- tion on the solvent-accessible molecular surface and in the protein core
669 5eo6 - A Molecular, Structural, and Cellular Multiple-Level Study Aimed at Understanding the Unique Reaction Catalyzed by the Last Enzyme in the Heme-Biosynthesis 2018 AIC Luna - 2018 - search.proquest.com Overlay of the structures of a representative heme b-bound chlorite dismutase and solvent This research aimed to understand ChdC function at the molecular, structural , and cellular levels The coproheme-bound ChdC structure revealed a helical-loop that is flexible and moves
670 3qk8 3q1t Functional Characterization of Structural Genomics Proteins through Computed Chemical Properties, Graph Representation of Active Sites, and Biochemical 2018 CL Mills - 2018 - search.proquest.com These five proteins were purified separately using the same protocol: two putative enoylCoA hydratases from Streptomyces avermitilis (PDB 3GKB, gene echA1; PDB 3H0U, gene echA2), putative 3-hydroxybutyryl-CoA dehydratase from Rhodopseudomonas palustris (PDB 3HIN, gene RPA1786), putative enoyl-CoA hydratase from Mycobacterium avium (PDB 3Q1T, gene MAV_3574), and putative enoyl-CoA hydratase from Mycobacterium marinum (PDB 3QK8, gene echA15).
671 3gvh - Analysis of the Mycoplasma bovis lactate dehydrogenase reveals typical enzymatic activity despite the presence of an atypical catalytic site motif 2018 Y Masukagami, KA Tivendale- , 2018 - mic.microbiologyresearch.org between MBOVPG45_0326 and the other bac- terial LDHs, and 2230 % identity across the region of align- ment between MBOVPG45_0326 and the other bacterial and parasitic MDHs in the PDB protein structure database 3GVH RCSB PDB Brucella melitensis LDH
672 4n5f - Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family 2018 T Schwander, R McLean, J Zarzycki, TJ Erb- Journal of Biological, 2018 - ASBMB The structure was solved using molecular replacement using the Phaser-MR and AutoBuild programs of the Phenix software package (31). The structure of a putative acyl-CoA dehydrogenase (PDB code 4N5F; 26.5% sequence identity) served as a search model for the molecular replacement.
673 3kw3 - Identification of a new alanine racemase in Salmonella Enteritidis and its contribution to pathogenesis 2018 S Ray, S Das, PK Panda- Gut pathogens, 2018 - gutpathogens.biomedcentral.com From I-Tasser and BLAST analyses, SEN4016 (359 amino acid residues) showed significant structural identity of 91% with Chain A, Y274f Alanine Racemase from E. Coli (PDB-ID-4WR3) with an estimated score of 0.97 ± 0.05 and C-score of 1.82. Similarly, SEN3897 having a score of 0.85 ± 0.08 and C score of 1.00 showed 42% identity with Chain A, Alanine Racemase from Bartonella henselae (PDB-ID-3KW3) and SEN1235 with a C score of 1.79 and estimated score of 0.97 ± 0.05 showed 48% identity with chain A of alanine r
674 3slg 3i3f, 3dah, 3inn, 3hm0, 4pca, 5udf, 4q1t, 5w15, 3ld9, 4ghk, 5kak, 3l0g, 4lgv, 5bq2, 3t3w, 4lgo, 5dle, 4dz4, 3tk8, 3swo 5.1 Creation of Homo Multimer Protein Complex Dataset 2018 P Kangueane, C Nilofer- Protein-Protein and Domain-Domain Interactions - Springer 3LYU, 3M1R, 3MBH, 3MQ1, 3MW9, 3N2N, 3NWY, 3OVG, 3OZB, 3PW3, 3SBA, 3SLG , 3T3W, 3T94 Distribution of homo multimer protein complex structures at the protein data bank ( PDB ) 5.3 Structure of a homo trimer glycosidase (1AM7) from enterobacteria phage lambda is
675 3gmt - Approaches for studying allostery using network theory 2018 M Hodges - 2018 - spiral.imperial.ac.uk 101 6.9 Optimization of coherent active and allosteric site motion in 3-dimensional structure . . . 102 B.1 DBSCANmethodforclustering a structural basis for allostery based on comparisons of active and inactive structures . The concept of struc
676 4ix8 - Bioinformatic analysis of the fold type I PLPdependent enzymes reveals determinants of reaction specificity in lthreonine aldolase from Aeromonas jandaei 2018 K Fesko, D Suplatov, V vedas- FEBS open bio, 2018 - Wiley Online Library to account for structural and functional variability within a large superfamily. First, comparison of protein structures was implemented to study distant evolutionary relationships because structures are more conserved in evolution than sequences. Table 1. Conserved and FSPs in the aspartate aminotransferase superfamily. Tyrosine aminotransferase 4ix8 D253
677 5u9p 3ftp Electrical Supporting information 2018 F Sha, Y Zheng, J Chen, K Chen, F Cao, M Yan - pdfs.semanticscholar.org Entry Enzyme GenBank accession no. Amino acid identities with PspPDH [%] Template PDB code TM- scorea Gbind [kcal mol-1] 23 PhpPDH WP_045028254 41.53 4z9y 0.90 -5.71 1.96 24 DfPDH WP_050774712 31.98 5u9p 0.90 -11.90 2.01
678 3o0h - Sulfur (lone-pair) interactions with FAD in flavoenzymes 2018 RFN Silva, ACS Sacco, I Caracelli- Zeitschrift fr, 2018 - degruyter.com The interactions of π-systems with lone-pairs of electrons are known and have been described in biological systems, involving lone-pairs derived from metals, metalloids, sulphur, oxygen and nitrogen. This study describes a bibliographic survey of the disulphide-bound sulphur(lone-pair) interactions with -systems residing in the flavin ad Also, the S(lp)…π(FAD) interaction in the 1K4Q [64] and 3O0H [65] proteins show the orientation of sulphur-lp to the Ct(U) centroid, F
679 4lgv - Multi-Scale Simulation of Electrostatic Channeling 2018 Y Liu - 2018 - search.proquest.com Figure 2-6 (a) Illustration of the proposed channeling complex using a poly(lysine) bridge as an electrostatic surface between hexokinase (HK; PDB 3VF6) and glucose-6-phosphate dehydrogenase (G6PDH; PDB 4LGV). (b) Experimental reaction scheme used to study electrostatic channeling of the charge intermediate (glucose-6-phosphate) across a cationic peptide bridge.
680 4kyx - Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis 2018 J Liu, Z Guan, H Liu, L Qi, D Zhang, T Zou, P Yin- Molecular plant, 2018 - cell.com the structure by molecular replacement based on the available coordinates (MutT, PDB : 53 4KYX ) and refined the structure at a resolution of 1.39 (Supplemental Table 1). Most of 54 such as FPP. Furthermore, our findings provide new opportunities for structure -guided 156
681 4fry - Chromophorylation of cyanobacteriochrome Slr1393 from Synechocystis sp. PCC 6803 is regulated by protein Slr2111 through allosteric interaction 2018 Q He, QY Tang, YF Sun, M Zhou, W Grtner- Journal of Biological, 2018 - ASBMB Taking the crystal structure of Bammc 406_4587 (a putative signal-transduction protein with CBS domains from Burkholderia ambifaria MC40-6, pdb code: 4fry ) (26) as template, a three-dimensional model of Slr2111 was constructed (Fig. 2 BE)
682 4zju - Battling Antibiotic Resistance by Investigation of Acinetobacter baumannii Enoyl Acyl Carrier Protein Reductase 2018 C Wong - 2018 - scholarworks.csun.edu The active site residues of abFabI in green ( PDB ID: 4ZJU , ecFabI in blue ( PDB ID: 5CFZ) and InhA in magenta ( PDB ID: 4TRM) overlay relatively Bacterial Species Year Representative PDB ID FabI homologs are similar in sequence, but the structure of their active sites may
683 6ao8 - Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop 2018 P Stephen, S Ye, M Zhou, J Song, R Zhang- Journal of molecular, 2018 - Elsevier 14]), Campylobacter jejuni (3FNR, unpublished), Plasmodium falciparum (5JLD[15]), Neisseria gonorrhoeae ( 6AO8 , unpublished), Escherichia crystal structure of EcoArgRS in complex with tRNA Arg (deposited under PDB code: 5YYN) representing the first structure of a
684 3si9 3qfe Dihydrodipicolinate synthase is absent in fungi 2018 S Desbois, UP John, MA Perugini- Biochimie, 2018 - Elsevier Bacillus clausii, 3E96, Bartonella henselae, 3SI9 , [41] 2C) compared to the head-to-head architecture observed for bacterial tetramers (Fig. 2B). Recently, a crystal structure of a putative fungal DHDPS ( PDB ID: 3QFE) has been deposited in the Protein Data Bank ( PDB ) (Fig
685 2lxf - Machine Learning-assisted Prediction of Structure and Function of Cystine-stabilized Peptides and Optimization of Expression in an E. coli System 2018 SMA Islam - 2018 - search.proquest.com Each type is annotated with its name, PDB id, function and jmol estimated average 3D structural distance between disulfide bonds PBS Phosphate buffered saline PDB Protein data bank QSAR Quantitative structure activity relationship QSO Quasi-sequence-order
686 4qfh - Identificao e caracterizao de inibidores da enzima glicose-6-fosfato isomerase de Leishmania mexicana 2018 SGR Mota - 2018 - repositorio.unicamp.br A computational analysis of cavities present on LmPGI crystallographic structure suggests a potential binding site for the inhibitors PBS Phosphate Buffer Solution PDB Protein Data Bank SSGCID Seattle Structural Genomics Center for Infectious Diseases
687 4q15 - Development of METALACTIVE SITE and ZINCCLUSTER tool to predict active site pockets 2018 M Ajitha, K Sundar, S Arul Mugilan- Proteins: Structure, 2018 - Wiley Online Library As zinc ion acts as a cofactor for this protein, ZN and PDB ID (3CAJ) of this of Sobolev et al.,[14] who identified the presence of Zinc using three-dimensional structure and he 1Q15, 0.86, 2Q15, 0.86, 3Q15, 0.84, 4Q15 , 0.28, 5Q15, 0.86, 6Q15, 0.86, 7Q15, 8.86, 8Q15, 0.86, 9Q15
688 4efz - Structural and Mechanistic Characterization of Enzymes in Persulfide Oxidation and Monolignol Biosynthesis Pathways 2018 SA Sattler - 2018 - search.proquest.com of apo-form PpPDO2 diffraction data were conducted by molecular replacement with the PDB coordinates of model 4EFZ using PHENIX Phaser (18) by molecular replacement as well, using the atomic coordinates of the unpublished structure for a
689 3rmi 4kzp, 4gt1, 4q04 Prediction of Homodimeric Residue-residue Contacts Through Co-evolutionary and Sequence-based Analysis 2018 Y Hsieh - 2018 - edepot.wur.nl 1000 residue range, and a quick pass of the identifiers through RCSB PDB's web-based However, we do not perform any sort of structural alignment to filter out structurally similar the case that this choice biases our dataset towards a certain type of structure , therefore impacting
690 5vaz - DnaG PrimaseA Target for the Development of Novel Antibacterial Agents 2018 S Ilic, S Cohen, M Singh, B Tam, A Dayan, B Akabayov- Antibiotics, 2018 - mdpi.com 3. Structural Features of DnaG Primase: Opportunities for Drug Targeting IDs: 2HAJ, 1T3W [38,41], respectively, S. aureus PDB ID: 2LZN [42], and Vibrio cholera PDB ID: 4IM9 The crystal structure of the complex between the C-terminal part of DnaG (HBD) and the N-terminal
691 4g5d 4gie A role for trypanosomatid aldo-keto reductases in methylglyoxal, prostaglandin and isoprostane metabolism 2018 AJ Roberts, J Dunne, P Scullion, S Norval- Biochemical, 2018 - biochemj.org Multiple sequence alignment of SakRI, TcAKR (TcCLB.511287.49), LiPGFS1 (LinJ.31.2210), LiPGFS2 (LinJ.32.0470) and TbPGFS (Tb927.11.4700). The conserved AKR catalytic tetrad identified in T. brucei is marked by the red boxes. Blue boxes indicate solvent accessible cysteine residues identified in the crystal structures of TbPGFS TcAKR and LiPGFS2 (PDB accession numbers 1VBJ, 4GIE and 4G5D) [27]. Orange box highlighting Y51C allelic variation was observed in CL-Brener.
692 5udf - Insights into bacterial lipoprotein trafficking from a structure of LolA bound to the LolC periplasmic domain 2018 E Kaplan, NP Greene, A Crow- Proceedings of the, 2018 - National Acad Sciences Fig. 4. Structural and bioinformatic evidence that the Hook is conserved among LolC, LolE, and LolF but absent from the wider type VII ABC transporter superfamily. Comparison of the periplasmic domains of A. actinomycetemcomitans MacB (5LIL), Mycobacterium tuberculosis FtsX (4N8N), E. coli LolC (5NAA), and A. baumannii LolF (5UDF, annotated as LolE in the PDB).
693 4z9n - Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics 2018 M Otzen, C Palacio, DB Janssen- Applied microbiology and biotechnology, 2018 - Springer 4282 5 1154 Acyl-CoA dehydrogenase 42, Thermus thermophilus 1.3.99.2 2DVL 2532 28 1031 ABC transporter, amino acid binding protein 59, Brucella ovis 4Z9N 3504 39 1922 Serine protein kinase 77, E. coli 2.7.11.1 P0ACY5
694 5ihp - Structural studies of the DNA partitioning protein IncC from the plasmid RK2 2018 MFU Rehman - 2018 - etheses.bham.ac.uk Page 1. Structural Studies of the DNA Partitioning Protein IncC from the Plasmid RK2 By 251 6.15.2 Crosslink- structure mapping using IncC2 models 23 1.16 Structures of DNA/centromere binding proteins (CBP) 25 1.17 C- and N- terminals of KorB protein
695 3qh8 3py5, 3py6 An unusual diphosphatase from the PhnP family cleaves reactive FAD photoproducts 2018 GAW Beaudoin, Q Li, SD Bruner, AD Hanson- Biochemical Journal, 2018 - biochemj.org Skip to main content. Main menu. Home; About the Journal: Scope; Editorial Board; Impact & Metrics; Benefits of Publishing; Advertising/Sponsorship; About the Biochemical Society. Current Issue; For Authors: Submit Your Paper; Submission
696 4yk1 - High performance computing with coarse grained model of biological macromolecules 2018 EA Lubecka, AK Sieradzan, C Czaplewski- Supercomputing, 2018 - superfri.org The source code in the UNRES package with Fortran 90 has the following directory structure : unres (main program modules, source NucB (110 residues, single chain, PDB code: 5OMT), BID domain of Bep6 (137 residues, single chain, PDB code: 4YK1 ), CDI complex
697 5vog 4mh4 Phase Combination and its Application to the Solution of Macromolecular Structures: Developing ALIXE and SHREDDER 2018 CL Milln Nebot - 2018 - tdx.cat Table 1 Test set for performance evaluation of SHREDDER and ALIXE... ID PDB 5VOG solvent content
698 3p96 - Identification of Novel Drug Target Pathways and Scaffolds to Combat Tuberculosis 2018 A Garima - 2018 - ir.inflibnet.ac.in of Porphyromonas gingivalis into host cells by modulating host cytoskeletal architecture , innate immune of SerB1- and SerB2-modeled proteins over 3FVV and 3P96 , respectively, resulted The superimpositions of SerB1 and SerB2 models over HPSP crystal structure resulted in
699 5vnx 5jay Riemerella anatipestifer AS87_RS09170 gene is responsible for biotin synthesis, bacterial morphology and virulence 2018 X Ren, X Wang, H Shi, X Zhang, Z Chen, KK Malhi- Scientific reports, 2018 - nature.com 1DJE [30.2% identity]), Burkholderia multivorans ( PDB accession no. 5VNX [28.6% identity]) and Mycobacterium smegmatis ( PDB accession no. 3WY7 [29.9% identity]) 6). WT Yb2 cells were integral with clear structures , and few were undergoing division
700 3sth - Molecular Adaptations in Extremely Halophilic Protists 2018 T Harding - 2018 - dalspace.library.dal.ca proteins compared to the templates used to model the tertiary structures , as a of proteins and alteration of transcriptional programs, leading to modification of cell structure properties like open reading-frame OTU operational taxonomic unit P2XR P2X receptor PDB Protein Data
701 4g67 4f3n Proteobacterial Origin of Protein Arginine Methylation and Regulation of Complex I Assembly by MidA 2018 UFS Hameed, O Sanislav, ST Lay, SJ Annesley- Cell reports, 2018 - Elsevier (A) Secondary structure representation of the MidA crystal structure bound to SAH (E) Superimposition of MidA (green) onto the putative protein Q6N1P6 ( PDB : 1zkd) from R. palustris (orange) and ACR COG1565 ( PDB : 4g67 ) from B. thailandensis (purple); RMSD = 1.68
702 4h4g - Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional -oxidation reversal 2018 JM Clomburg, SC Contreras, A Chou, JB Siegel- Metabolic, 2018 - Elsevier The PDB codes for the 10 matches with the lowest E-values are 4H4G , 1U1Z, 4I83, 2OKH, 1ZHG, 3D6X, 2GLL, 3B7J, 1Z6B, and For ACP, the structure coordinated from an established structure of ACP bound to the homologous protein FabA was used ( PDB code: 4KEH)
703 6ape - Estudos estruturais e funcionais da enzima N5, N10-metilenotetrahidrofolato-desidrogenase-ciclohidrolase de Xanthomonas albilineans aplicados descoberta de 2018 RV Bueno - 2018 - teses.usp.br The structural , kinetic, and biophysical data obtained in this PhD thesis provide the molecular basis PCR Reao em cadeia da polimerase PDB Protein Data Bank PEG Polietilenoglicol SAR Relaes estrutura-atividade SBVS Structure -Based Virtual Screening
704 3r4t 4ffc QSAR and Molecular Docking Studies of the Inhibitory Activity of Novel Heterocyclic GABA Analogues over GABA-AT 2018 J Rodrguez-Lozada, E Tovar-Gudio- Molecules, 2018 - mdpi.com We have previously reported the synthesis, in vitro and in silico activities of new GABA analogues as inhibitors of the GABA-AT enzyme from Pseudomonas fluorescens... To incorporate the prosthetic group (PLP) in the homology models an alignment employing a crystal structure that possessed the PLP was done (3r4t and 1ohw for the Pseudomonas and human models respectively).
705 4wbs - Genetic investigation of how an ATP hydrolysis cycle is coupled to lipopolysaccharide transport 2018 BW Simpson - 2018 - rave.ohiolink.edu 36 1.3.1 Architecture of the ABC transporter family ..... 36 118 3.3.7 Crystallography data processing and structure determination ..... 118 6 Figure 1.3 MsbA undergoes structural conformational changes proposed to mediate LPS flipping This open dimer has also been observed for structures of LptB captured in the apo-state (PDB 4WBS, unpublished),
706 4ed9 - Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress 2018 KS Shrimant, S Pandey, A Ansari, S Das- et Biophysica Acta (BBA, 2018 - Elsevier The structure was found similar to the homologues available including MCR ( PDB ID: 1X74), CaiB ( PDB ID: 1XA3), FRC ( PDB ID: 2VJQ), FRC ( PDB ID: 3UBM), ACOCT ( PDB ID: 4ED9 ), YfdE ( PDB ID: 4HL6 3.5. Solution structure using Small Angle X-ray Scattering (SAXS).
707 4gnv - A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to -lactams in Pseudomonas 2018 LA Ho, JL Winogrodzki, AW Debowski- Chemical, 2018 - pubs.rsc.org Fig. 2 Crystal structure of BcNagZ bound to 2. (A) Electron density (sigma-A weighted difference map (mF o DF c ) contoured at 4) for 2 (green carbon atoms (B) BcNagZ active site bound to 2 (green carbon atoms) with the BcNagZ product complex PDB 4GNV superposed
708 4dxl - Oxadiazole and phenol derivatives as antibacterial and/or herbicidal agents 2018 TJ Hagen, M Thompson, JR Troxell- US Patent App. 15, 2018 - Google Patents To date, there are 17 crystal structures of six different species of IspE deposited in the PDB with 17 different ligands FIG. 11 . X-Ray Crystal Structure of Mycobacterium abscessus IspE with ATP (red) and CMP (blue) Bound to Active Site; PDBID 4DXL . FIG. 12
709 4xk1 - Structural analysis of phosphoserine aminotransferase (isoform 1) from Arabidopsis thalianathe enzyme involved in the phosphorylated pathway of serine 2018 B Sekula, M Ruszkowski, Z Dauter- Frontiers in Plant Science, 2018 - ncbi.nlm.nih.gov identity (Supplementary Figure S2), which are structurally very similar to AtPSAT1: PaPSAT ( PDB ID: 4xk1 , rmsd = 1.0 For example, in the structure of HsPSAT ( PDB ID: 3e77), the N-terminal coil at first look Residues 816 visible in the structure came from the expression tag
710 5b8i - Wen-Luo-Tong Decoction Attenuates Paclitaxel-Induced Peripheral Neuropathy by Regulating Linoleic Acid and Glycerophospholipid Metabolism Pathways 2018 F Wu, W Xu, B Deng, S Liu, C Deng, M Wu- Frontiers in, 2018 - ncbi.nlm.nih.gov The structures of proteins were obtained from the Protein Data Bank ( PDB , https://www.rcsb.org/). Protein structures not available from PDB was homology modeled by (https://www.swissmodel. expasy.org) docking was carried out with Discovery Studio 3.5 (BIOVIA, USA) Table 6 Results of docking Proteins PDB ID pcat1 5b8i *Template of homology modeling.
711 3r4t - Modeling and Docking Study of GABA-AT Protein in Mycobacterium Tuberculosis-A Computational Approach 2018 R Sriroopreddy, P Raghuraman- Research Journal of, 2018 - search.proquest.com The best similarity match with the template identity of 83% ( PDB ID: 3R4T ) The secondary structure prediction was done using YASPIN server (http://zeus.few.vu.nl/).8 The result of the secondary structure prediction provides a brief idea about the folding pattern of the
712 4nbr - MRREX: molecular replacement by cooperative conformational search and occupancy optimization on lowaccuracy protein models 2018 JJ Virtanen, Y Zhang- Acta Crystallographica Section D, 2018 - Wiley Online Library et al., 2016, 2017; Shrestha & Zhang, 2015), MR-REX takes advan- tage of this fact by predicting possible inaccurate segments of the structural model and Input and output data The input to MR-REX is a set consisting of structure -factor data, a structure file in PDB format and
713 5bnt - Structure of aspartate semialdehyde dehydrogenase from Francisella tularensis 2018 NJ Mank, S Pote, KA Majorek- Section F: Structural, 2018 - Wiley Online Library NADP+ (yellow spheres) is modeled using the structure of H. influenzae ASADH ( PDB PDB entry 3pzr; Pavlovsky et al., 2012), Pseudomonas aeruginosa ( PDB entry 5bnt ; Seattle Structural entry 1t4b; Nichols et al., 2004) and Haemophilus influenzae (HiASADH; PDB entry 1pqu
714 4ot8 - Chemoenzymatic synthesis of peptide beta-lactones and beta-hydroxy acids 2018 TA Wencewicz, JE Schaffer, MR Reck- US Patent App. 15/921,442, 2018 - Google Patents Although the biological target of RC-Obi is unknown, bacterial transpeptidases are thought to be potential targets due to the structural similarity of RC-Obi to monocyclic -lactam antibiotics and the FIG. 14D is an X-ray crystal structure of the EntF TE domain ( PDB 3TEJ). FIG
715 5thw 5i4m, 4wjb A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase 2018 T Sommer, K Bjerregaard-Andersen, L Uribe- Scientific reports, 2018 - nature.com with a central scaffold resembling the swivelling // fold 18 , while the majority of AHS members contains a monomeric (/) 8 -TIM like-barrel structural fold 19 The finalised model and structure factors were deposited to Protein Data Bank ( PDB ) and given the PDB
716 5cc8 - Transition from classical methods to new strategies: Mechanistic evaluation of inhibitors against Mycobacterium tuberculosis shikimate kinase 2018 N Ren Fuanta - 2018 - etd.auburn.edu of each family. As stated previously, structural information and interactions with substrate(s) or Group Family and members Example Structure Group 1: Protein S/TY kinase/ atypical protein kinase/ lipid kinase/ ATP- grasp Thiamine-monophosphate kinase PDB : 5CC8 (50)
717 4hvt - Pyrococcus furiosus Prolyl Oligopeptidase: A Dynamic Supramolecular Host for Peptidase and Dirhodium Catalysis 2018 K Ellis-Guardiola, H Rui, R Beckner, P Srivastava - 2018 - chemrxiv.org both Pfu POP and the S447C mutant possess a two-domain architecture involving a peptidase domain reported homology model; M. xanthus chain A from 2BKL; R. typhi from 4HVT ; S. Scrofa from 1QFS; H. Page 17 S1). The structure of
718 3s6d - Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB 2018 M Garton, S Nim, TA Stone, KE Wang- Proceedings of the, 2018 - National Acad Sciences Physiology; Plant Biology; Population Biology; Psychological and Cognitive Sciences; Sustainability Science; Systems Biology. Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB
719 4emd 4dxl, 4ed4 Evaluation of IspE for inhibitor design in the non-mevalonate pathway 2018 KB Hoerchler - 2018 - commons.lib.niu.edu crystal structures were obtained ( PDB : 1UEK, 1OJ4).38,39 IspE possesses structural features Figure 1-5. Crystal Structures of MaIspE The left structure ( PDB : 4EMD ) co-crystallized with CMP and a sulfate ion while the right ( PDB : 4ED4) co-crystallized with ATP.42
720 4f4h 5kha Kinetics and structural features of dimeric glutamine-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites 2018 ARS Santos, ECM Gerhardt, VR Moure- Journal of Biological, 2018 - ASBMB Given the availability of a 1.7 resolution structure of dimeric NadE2 Gln from B. thailandensis ( PDB code 4F4H ) obtained by the Burkholderia structome project (21), we used this protein to analyze the structural features of the subgroup of dimeric NadE2 Gln
721 3rd5 - Mechanistic Studies on the Light-Dependent NADPH: Protochlorophyllide Oxidoreductase and Animal Cryptochromes 2018 N Archipowa - 2018 - search.proquest.com a C15-E-anti-configuration as shown in Figure 1.4A [8]. This is followed by formation. of several thermally activated intermediates comprising structural changes of the POR. Crystal structure of the NB-protein catalytic site ( PDB : 3AEK [32]). The
722 3qh4 - Microbial esterases and ester prodrugs: An unlikely marriage for combating antibiotic resistance 2018 EM Larsen, RJ Johnson- Drug development research, 2018 - Wiley Online Library Bacterial esterase structure and function The bacterial esterase, LipW from M. tuberculosis ( PDB ID: 3QH4 ) is shown as an example with its sheets in tan, its helices in purple, and its catalytic triad in sticks and labeled
723 4hwg 5dld The tetrameric structure of sialic acidsynthesizing UDP-GlcNAc 2-epimerase from Acinetobacter baumannii: A comparative study with human GNE 2018 TP Ko, SJ Lai, TJ Hsieh, CS Yang, Y Chen- Journal of Biological Chemistry, 2018 - ASBMB known for at least 10 species ( PDB codes 1F6D, 1O6C, 1V4V, 3BEO, 3DZC, 3OT5, 4HWG , 4NEQ, 5DLD Structural determination and refinement molecular replacement with the PHENIX AutoMR (24) using the previously published human homologue structure ( PDB code 4ZHT
724 3meq - Activity-Related Microsecond Dynamics Revealed by Temperature-Jump Forster Resonance Energy Transfer Measurements on Thermophilic Alcohol 2018 MB Vaughn, J Zhang, TG Spiro, RB Dyer- Journal of the, 2018 - ACS Publications protein motions. figure Figure 1. Structure of ht-ADH in green with NADH and alcohol in cyan. The three tryptophan residues are yellow. This structure was created from an overlap of PDB : 1RJW and 3MEQ . The steady state
725 3oa1 - Modelado molecular de la fosfoprotena del virus de la rabia 2018 EM Dvila Gonzlez - 2018 - 148.204.103.62 De los servidores de NCBI y PDB se obtuvo la secuencia consenso, as como los templetes del alineamiento del monomero del virus de la rabia (azul) con el cristal 3OA1 (amarillo AAV Albertini, GS, W Weissenborn, RWH Ruigrok, Structural Aspect of Rabies Virus Replication
726 4q4l - Integrating cross-linking experiments with ab initio protein-protein docking 2018 T Vreven, DK Schweppe, JD Chavez, CR Weisbrod- J Mol Biol. 2018 Jun 8;430(12):1814-1828. For the resulting complex list, we then searched the PDB for unbound structures A method for integrative structure determination of protein-protein complexes 2636. [13] Pons C, D'Abramo M, Svergun DI, Orozco M, Bernad P, Fernandez-Recio J. Structural characterization of
727 3s6l 3njb, 3p96, 3km3, 3k9g, 3men, 3oib, 3o2e Substructure determination using phase-retrieval techniques 2018 P Skubk- Acta Crystallographica Section D: Structural Biology, 2018 - scripts.iucr.org determination by PRASA has been integrated into the CRANK2 pipeline for automated structure solution from 3fki, 3gyv, 3k9g, 3km3, 3lmt, 3lmu, 3men, 3njb, 3o2e, 3oib, 3p96, 3s6l , 4us7, 4xvz the authors who kindly provided SAD data sets or deposited Bijvoet pairs in the PDB
728 5v6d - A Centipede Toxin Family Defines a New Ancient Class of CS Defensins 2018 TS Dash, T Shafee, PJ Harvey, C Zhang- Available at SSRN, 2018 - papers.ssrn.com structure of Sm2 against all structures of proteins contained within the Protein Data Bank ( PDB ) that are composed of more than 30 amino acids Thus, the minimal cysteine motif is by itself sufficient to generate a stable CS structure . Although the 2ds-CS architecture has
729 4maq - The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria 2018 AKH Weiss, JR Loeffler, KR Liedl- Biochemical Society, 2018 - biochemsoctrans.org Skip to main content. Main menu. Home; About the Journal: Scope; Editorial Board; Benefits of Publishing; Impact & Metrics; Advertising/Sponsorship; About the Biochemical Society. Current Issue; For Authors: Submit Your Paper; Submission
730 3iew - Synthesis and Computational Analysis of Novel IspF Inhibitors 2018 D Harper, M Rouffet, L Votapka- Bulletin of the American, 2018 - pointloma.whdl.org The crystal structure of IspF was taken from the Protein Data Bank, code 3iew .7 The first As for the protein, the monomer's crystal structure was cleaned and protonated with the H++ webserver (version 3.2).11 The . pdb file was manually edited to correct these protonation states
731 3sbx 3qua Structural insight into molecular mechanism of cytokinin activating protein from Pseudomonas aeruginosa PAO1 2018 H Seo, KJ Kim- Environmental microbiology, 2018 - Wiley Online Library 29.9), Mycobacterium marinum (MmLOG, PDB code 3SBX , Z-score 28.7), Mycobacterium PDB code 5AJU, Z-score 27.2), with amino acid identities higher than 40%. In contrast, the structure of PA4923 shows relatively low homology to type-II LOGs, such as those from
732 5idv - Synthesis, spectroscopic properties, crystal structure, antimicrobial properties and Molecular Docking Studies of the complex (1) 3 (C36H24MnN6) 6 (PF6). 0.5 H2O 2018 HEL Hamdani, MEL Amane, C Duhayon- Journal of Molecular Structure, 2018 - Elsevier Docking studies was proceeded by taking the five receptors (The PDB id: 1E15(S 3BU2 (S. saprophiticus), 3GFX (klipsila pnumani), 1BY3 (E. coli) and 5IDV (acinetobacter baumannii determination of complex (1) confirmed the assignments of the structure from spectroscopic data
733 3dmp - Enzymatic Production of NonNatural Nucleoside5Monophosphates by a Thermostable Uracil Phosphoribosyltransferase 2018 J del Arco, J Acosta, HM Pereira, A Perona- , 2018 - Wiley Online Library Overall structure and architecture of active site. We have determined the crystal structure of TtUPRT ( PDB 1v9s) at 2.1 resolution (Table 1). The 1o5), UPRT from Escherichia coli (EcUPRT; PDB 2ehj), UPRT from Burkholderia pseudomallei (BpUPRT; PDB 3dmp ), UPRT from
734 3v2i 4f3y, 4dz4 A Computational Biology Approach in Function Annotation to Enzymes 2018 M Ljubijankic- Southeast Europe Journal of Soft Computing, 2018 - scjournal.ius.edu.ba 3.5.3.1 2Q47 3.1.1.3 3.1.3.48 3SF8 3.1.6. 3.4.-.- 3V2I 3.4.19.12 3.1.1.29 is observed in the example of the survival protein E (SurE) from Thermotogamaritima ( PDB ID 1ilv). Zhang and colleagues (2001) determined the crystal structure of this protein and in their work, described it
735 3v9o 3urr Flexible backbone assembly and refinement of symmetrical homomeric complexes 2018 SSR Burman, RA Yovanno, JJ Gray- bioRxiv, 2018 - biorxiv.org For local docking, specific symmetry definitions can be recapitulated from a PDB file of a complex About 22% of all structures are unfavorable, and all but one near-native (less than 5 number of inter-chain atom-atom clashes is 50.6, compared to 21 in the native structure
736 3sdo - Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the 4S Desulfurization Pathway 2018 T Su, J Su, S Liu, C Zhang, J He, Y Huang- Frontiers in, 2018 - frontiersin.org This work combined with our previous structure of DszC provides a systematic structural basis for the The native BdsA structure was resolved by molecular replacement using Phaser from the CCP4 suit of programs (Winn et al., 2011) with LadA ( PDB entry 3B9N) as the
737 4wec - Quantitative proteomic and transcriptional analyses reveal degradation pathway of -hexachlorocyclohexane and the metabolic context in the actinobacterium 2018 PE Sineli, HM Herrera, SA Cuozzo, JSD Costa- Chemosphere, 2018 - Elsevier Template crystal structures , obtained from PDB data bank (RCSB- PDB ), were 3A76 for dehydrochlorinase, 4HZG for haloalkane dehalogenase and 4WEC for short-chain alcohol dehydrogenase. Protein structures were visualized using PyMol
738 4xwi - Towards novel inhibitors against KdsB: A highly specific and selective broad-spectrum bacterial enzyme 2018 S Ahmad, S Raza, A Abro, KR Liedl- Biomolecular Structure, 2018 - Taylor & Francis from Protein Data Bank ( PDB ) with PDB ID, 4FCU (Berman et al., 2006). The protein is present (A. baumannii), 3K8D (E.coli), 4XWI (P. aeruginosa), 3TQD (C. Burnetii), 3QAM (V explicates enzyme structure stability and strong binding affinity of the compound towards the
739 5idw - Structure and characterization of a NAD(P)Hdependent carbonyl reductase from Pseudomonas aeruginosa PAO1 2017 S Li, X Teng, L Su, G Mao, Y Xu, T Li, R Liu- FEBS, 2017 - Wiley Online Library NADP binding induces structural changes including the ordering of the active site specificity loop, and the presence of small molecules The native PA4079 structure was determined by molecular replacement with phaser 14 in the phenix suite 15 using PDB entry 3WXB
740 4kna - Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket 2017 JH Bertram, KM Mulliner, K Shi - Applied and , 2017 - Am Soc Microbiol ... The closest homologous structures currently available are those reported under PDB accession no. 4KNA (N-succinylglutamate 5-semialdehyde dehydrogenase from Burkholderia thailandensis) and 3JU8, with amino acid sequence identities of 63% and 62%, respectively. ...
741 5j49 - Glucose-1-phosphate uridylyltransferase from Erwinia amylovora: Activity, structure and substrate specificity 2017 S Benini, M Toccafondi, M Rejzek, F Musiani- et Biophysica Acta (BBA, 2017 - Elsevier A summary of data collection and refinement parameters are reported in Table 1. Coordinates and structure factors have been deposited in the PDB with accession code:4D48. A search for structural similarity in the PDB was carried out with PDBeFold [46] Table 4. Glc-1P uridylyltransferase 5J49 B. xenovorans
742 5enu - An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins 2017 AF Harper, JB Leuthaeuser, PC Babbitt - PLOS Computational , 2017 - journals.plos.org ... the PFAM family, and structural modelling to create active sites; ultimately structural comparisonsare ...Notably, the invariant Gly, Ser, and Asp of the G(V/I)SxD motif are all in the 5ENU active site, along with the conserved Leu. These distinctive features suggest that, indeed, these two subgroups are functionally distinct.. ...
743 4k6f - Cloning, expression and molecular modeling of the anthocyanidin reductase (FaANR) gene during strawberry fruit development 2017 PC Mandave, AA Kuvalekar, NL Mantri, MA Islam - 2017 - repository.up.ac.za on 3D structure of ANR obtained from homology modeling technique to check binding interaction of template molecule ( PDB ID: 4K6F ) with bound Their complex structure limits the com- mercial chemical synthesis and we are therefore highly re- liant on plants, especially
744 3ijp - Plant DHDPR forms a dimer with unique secondary structure features that preclude higher order assembly 2017 SAJ Watkin, JR Keown, E Richards- Biochemical, 2017 - biochemj.org Cirilli, M., Zheng, RJ, Scapin, G., and Blanchard, JS (2003) The three-dimensional structures of the Structural and mutagenic analysis of relaxed nucleotide specificity Scapin, G., Reddy, SG, Zheng, R., and Blanchard, JS (1997) Three-dimensional structure 490 of Escherichia
745 5i3e - Benzoyloxy-ethyl-carbamic acid: A novel anticancerous secondary metabolite produced by Streptomyces globosus VITLGK011 2017 L Ravi, K Krishnan - 2017 - nopr.niscair.res.in A total of 11 drug target proteins were chosen and the 3D structure was downloaded from PDB website (www.rcsb.org) with the following PDB -ID: 5JSN, 5FMJ, 5J9Y, 2YJA, 3G73, 5FWL, 5I3E , 5JSB, 3S4E, 5HA9, and 5HHD. Downloaded protein structures were prepared for
746 4q1t - CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum 2017 Y Jiang, F Qian, J Yang, Y Liu, F Dong, C Xu- Nature, 2017 - nature.com ... 5b). Assuming that D154 and N155 of cgProB are part of the active site, 3D protein structure modelling indicated that five amino-acid residues (G149, G153, D154, N155, and D156) participate in a complex hydrogen-bonding network with L-proline (Fig. 5b). ... The three-dimensional structural model of cgProB was generated through homology modelling using the SWISS-MODEL server40,41,42 (https://swissmodel.expasy.org/). The available structure of btProB (PDB code: 4q1t, which shares 38% sequence similar
747 5ids - Mrub_2052, Mrub_0628, and Mrub_2034 genes are predicted to be orthologous to b0688, b2039, and b3789 genes found in Escherichia coli, which are involved in 2017 JP Hartnett, D Scott - 2017 - digitalcommons.augustana.edu (Finn et al.). Protein Data Bank ( PDB ) (Berman et. al., 2000) is a curated collection of crystalized proteins.If a PDB hit is obtained for a query sequence, then 3-D structure neighbors, Page 7. 6 PDB protein database 5IDS Glucose-1-phosphate Thymidylyltransferase
748 3v7o - Viral Shapeshifters: Strange Behaviors of HIV and Other Viruses 2017 GKM Goh - 2017 - books.google.com and www.ncbi.nlm.nih.gov. Jmol and CN3D were used in this book. Sequences and structural protein databank ( PDB ) files are available at www.ncbi.nlm.nih.gov Linus Pauling discov- ered a common helical structure , the alpha helix, among pro- teins
749 3o0m - The DNA repair repertoire of Mycobacterium smegmatis FenA includes the incision of DNA 5'flaps and the removal of 5'adenylylated products of aborted nick ligation 2017 ML Uson, S Ghosh, S Shuman- Journal of bacteriology, 2017 - Am Soc Microbiol MSMEG_5871 (Rv0759c) has not been characterized. MSMEG_5028 (Rv1262c) has been characterized structurally (PDB entry 3O0M), but its biochemical activity is uncharted.
750 4k9d 4l83 Review on Computational Approaches for Identification of New Targets and Compounds for Fighting Against Filariasis 2017 M Mishra, P Srivastava- The Open Bioactive Compounds, 2017 - benthamopen.com S100a12MMDB ID: 73787 PDB ID: 2WCF [Metal Binding Protein], Glyceraldehyde 3-phosphate dehydrogenase MMDB ID: 109769 PDB ID: 4K9D etc.) in In molecular biology and structural genomics, protein structure determination has become an important area of research
751 4kam - Metabolic engineering of O-acetyl-L-homoserine sulfhydrylase and Met-biosynthetic pathway in Escherichia coli 2017 Y Ma - 2017 - depositonce.tu-berlin.de ... secondary structure and overall stability of investigated proteins. All these reasons highlight ... Figure 2
752 4fkx - Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization 2017 AK Mishra, N Singh, P Agnihotri, S Mishra - Journal of Computer- , 2017 - Springer ... novel LaNDK inhibitors, the crystal structure of Leishmania major NDKb in complex with ADP(PDB ID: 3NGU ... three fold virtual screening uti- lizing Surflex-dock, GeomX and Flex-X, as ourstructure lacks the ... TbNDK (4FKX) 32,672 14,027 20,443 3566 32.7 6.6 Hexamer Dimer ...
753 3ido - A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases 2017 JB Bertoldo, T Rodrigues, L Dunsmore, FA Aprile- Chem, 2017 - Elsevier Using the FATCAT algorithm operating in rigid mode, we found that the structures of phosphatases from Vibrio cholera O395 (PDB: 4LRQ52), Entamoeba histolytica (PDB: 3IDO53), S. aureus (PDB: 3ROF54), ... and Geobacillus stearothermophilus (PDB: 4PIC) shared the highest structural similarity.
754 4noz - Functional and evolutionary characterization of Ohr proteins in eukaryotes reveals many active homologs among pathogenic fungi 2017 DA Meireles, RM Domingos, JW Gaiarsa, EG Ragnoni - Redox biology, 2017 - Elsevier ... (A) For Ohr, 4NOZ secondary structure from Burkholderia cenocepacia ... (C) Selected Ohr-likesequences deposited in PDB database were aligned with ... For Ohr-like, secondary structure 2PN2from Psychrobacter arcticus 273-4 (Pa_Ohr_like) was used to guide the alignment. ...
755 3p96 - Regulatory Mechanism of Mycobacterium tuberculosis Phosphoserine Phosphatase SerB2 2017 GA Grant- Biochemistry, 2017 - ACS Publications figure Figure 1. Ribbon diagram of the structure of M. avium phosphoserine phosphatase (maPSP, Protein Data Bank entry 3p96 ) (right panel). The enzyme is a dimer with each subunit consisting of a catalytic domain (dark
756 4iuj 3khw, 3r2v, 4p9a Current Drug Design Strategies for Fighting Against Swine Influenza 2017 M Alam, S Nandi- Current Drug Therapy, 2017 - ingentaconnect.com ... In-silico docking studies are at the fore front of structure based screening and designing of emerg- ing anti-swine ... PDB IDs of Crystal Structures ... 5D8U, 5D9J, 5DEB, 5DES, 5I13, 5CXR, 5FDD, 5FDG, 4ZQQ, 4ZHZ, 4ZI0, 4YYL, 4W9S, 4P9A, 4MK1, 4MK2, 4MK5, 4IUJ , 4F7M, 4AWK ...
757 4gl8 - Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter 2017 AM Groshong, A Dey, I Bezsonova, MJ Caimano- mBio, 2017 - Am Soc Microbiol Structural features distinguish BbOppA4 from Gram-negative and Gram-positive OBPs.We took advantage of the crystal structure of BbOppA4 ( PDB ID: 4GL8 ) (39) to determine if B. burgdorferi OBPs possess structural elements compatible with promiscuous peptide binding, the
758 4u7x - Mrub_3029, Mrub_2052, are predicted orthologs of b_0688, b_0394, while Mrub_0759 and Mrub_2365 are not predicted orthologs of b_1309, in Escherichia 2017 MA Benstine, D Scott, R Lori - 2017 - digitalcommons.augustana.edu Next, the Protein Data Bank ( PDB ) is accessed which gives 3-D models of protein structures our gene is found in, it helps portray how the protein is folded which helps predict function (Bernman et al, 2003) Protein Database ( 4U7X ) Crystal structure of Fructokinase from
759 4dlp - High Throughput Virtual Screening to Identify Novel natural product Inhibitors for MethionyltRNA-Synthetase of Brucella melitensis 2017 M Kumari, S Chandra, N Tiwari, N Subbarao - Bioinformation, 2017 - ncbi.nlm.nih.gov ... IV, and Methionine analogus dataset respectively. The crystal structure of MetRsBm(4DLP) was obtained from protein data bank (http://www.rcsb.org/pdb/explore.do?structureId=4DLP). The protein was prepared by removing ...
760 5umf - Design of synthetic symmetrical proteins 2017 JRH Tameb, ARD Voet- Synthetic Biology: Volume 2, 2017 - books.google.com assembly, Ribulose-phosphate structure but since exhibits alpha 3-epimerase, C and 2 PDB : 5UMF ) and 12-fold rotational symmetry (cartoon depiction; from left to right, PDB : 4YY2, 4YXX designs will without any doubt improve our understanding of protein structure and stability
761 4tu1 - Isomer Activation Controls Stereospecificity of Class I Fructose-1, 6-bisphosphate Aldolases 2017 PW Heron, J Sygusch- Journal of Biological Chemistry, 2017 - ASBMB At the structural level, there is complete conservation of the subunit beta-barrel fold 1A) corresponds to an active site fully occupied by FBP that super- poses identically with the FBP bound structure of the rabbit homolog [ PDB ID: 1ZAI] (rms devia- tion = 0.41 based on
762 4j3g - Non-specific activities of the major herbicide-resistance gene BAR 2017 B Christ, R Hochstrasser, L Guyer, R Francisco- Nature plants, 2017 - nature.com We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism... The search model was an ensemble model generated with Ensembler using eight protein structures homologous to BAR (PBD codes and % identity to BAR: 2JLM (28%), 3DR8 (35%), 4J3G (31%), 4JXQ (33%), 4MBU ...
763 4w65 - Functional analysis of a novel -(1, 3)-glucanase from Corallococcus sp. EGB containing a fascin-like module 2017 J Zhou, Z Li, J Wu, L Li, D Li, X Ye, X Luo - Applied and , 2017 - Am Soc Microbiol ... The GH16 domain sequence of LamC was aligned with the following proteins: β-(1,3)-glucanase A1 (GlcA) from B. circulans (accession no. P23903), ... and the glycoside hydrolase family protein from Mycobacterium fortuitum (PDB no. 4W65) ...
764 4dz4 - Characterising two genomic islands involved in metabolism in Neisseria meningitidis 2017 AJ Chu - 2017 - etheses.whiterose.ac.uk Figure 3.1-1 Simplified chemical structures of polyamines ----- 47 characterisation of the meningococcal pili structure demonstrates the organism's 135, X, Y, Z and 29E were duly classified based on structural variations in capsular
765 3meq - ENZYMATIC REDUCTION BY ALCOHOL DEHYDROGENASE TA1316 FROM Thermoplasma acidophilum 2017 M Guzmn-Rondrguez, L Santos - Revista Mexicana de Ingeniera , 2017 - redalyc.org ... 3MEQ Brucella melitensis ADH Tetramer Zn +2 , Cl, Na + 0.930 To be published 1R37 Sulfolobussolfataricus ADH Tetramer Zn +2 0.929 (Esposito et al. 2003) ... Structural analyses displayed by thePDB platform showed the crystal structure of Pyrobaculum aerophilum ...
766 3p10 - Characterization of The Binding Thermodynamics of Metal Cofactors to Burkholderia pseudomallei IspF 2017 KT Do - 2017 - commons.lib.niu.edu ... catalytic function. Figure 1: Crystal structure of Burkholderia pseudomallei IspF (PDB: 3P10).Yellow spheres indicate catalytic Zinc ions. Page 7. The ... cyan). A single protein crystalstructure (PDB ID: 3P10) is, depicted for clarity. Key interactions ...
767 2khp - Effects of novel fragment-warhead adducts in situ and in vitro with glutaredoxin orthologs. 2017 AJ Caras - 2017 - ideaexchange.uakron.edu ... Figure 1. Structure of RK088 ACP, an example of a fragment- warhead adduct. ... by pastmembers of Dr. Leeper's group.23 Figure 2. Solution structures of hGRX1 (PDB: 1JHB)29and BrmGRX (PDB: 2KHP)20, with the CPYC active-site motif magnified. ...
768 4u7x - Mrub_3029, Mrub_2052, are predicted orthologs of b_0688, b_0394, while Mrub_0759 and Mrub_2365 are not predicted orthologs of b_1309, in Escherichia coli, 2017 MA Benstine, D Scott, R Lori - 2017 - digitalcommons.augustana.edu ... Next, the Protein Data Bank (PDB) is accessed which gives 3-D models of protein structures ourgene is found in, it helps portray how the protein is folded which helps predict function (Bernmanet al, 2003). ... Protein Database (4U7X) Crystal structure of Fructokinase from ...
769 4ni5 - Crystal structure and iterative saturation mutagenesis of ChKRED20 for expanded catalytic scope 2017 FJ Zhao, Y Jin, Z Liu, C Guo, TB Li, ZY Li- Applied Microbiology, 2017 - Springer ... model was the monomer of Dehydrogenase from Brucella Suis ( PDB code 4NI5 ; NCBI accession ... Therefore, the determination of the crystal structure of ChKRED20 is crucial and greatly facilitates the ... high level of identity of ChKRED20 to typical SDRs in the PDB database, such ...
770 4xgi - Discovery of a Potentially New Subfamily of ELFV Dehydrogenases Effective for lArginine Deamination by Enzyme Mining 2017 W Wu, Y Zhang, J Huang, Y Wu, D Liu- Biotechnology, 2017 - Wiley Online Library Active site of glutamate dehydrogenase ( PDB 4XGI ) (A), phenylalanine dehydrogenase ( PDB 1BW9) (B), valine dehydrogenase ( PDB 1LEH) (C Phenylalanine was inserted into the active site of valine dehydrogenase (C) by structure alignment of 1BW9 and
771 4wxt 5uth Mecanismo de ao e infeco por Corynebacterium pseudotuberculosis: expresso, purificao e caracterizao de protenas relacionadas ao metabolismo central 2017 LA Kawai - 2017 - repositorio.unesp.br Page 9. PBS: Tampo fosfato contendo NaCl PDB : Protein Data Bank RMN: Ressonncia Magntica Nuclear Corynebacterium pseudotuberculosis: Role of Electrostatic Forces in the Stability of the Secondary Structure , minha contribuio foi realizada na reviso final, onde
772 3u0g - A Novel highly thermostable branched-chain amino acid aminotransferase from the crenarchaeon Vulcanisaeta moutnovskia 2017 TN Stekhanova, AL Rakitin, AV Mardanov - Enzyme and Microbial , 2017 - Elsevier ... The first X-ray diffraction structure of BCATs, namely, the structure of BCAT ... The search for close homologues of VMUT0738 using BLAST showed the highest levels of identity with hypothetical BCATs from other members of the genera Vulcanisaeta … The homologues with known structures were TUZN1299 from T. uzoniensis (PDB ID 5CE8, 54% identity, query cover 94%), putative BCAT from Burkholderia pseudomallei (PDB ID 3U0G, 47% identity, query cover 94% ...
773 5dwn - Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex 2017 EJ Loveridge, C Jones, MJ Bull, SC Moody - Journal of , 2017 - Am Soc Microbiol ... protein [37], including conservation of the bleomycin-binding regions), phosphinothricinN-acetyltransferase (36% identical to phosphinothricin N-acetyltransferase from Brucella ovis[GenBank accession number WP_006155257; PDB accession number 5DWN], with significant ...
774 4kna - Characterization of five fatty aldehyde dehydrogenase enzymes from Marinobacter and Acinetobacter: structural insights into the aldehyde binding pocket 2017 JH Bertram, KM Mulliner, K Shi - Applied and , 2017 - Am Soc Microbiol ... Furthermore, we 70 selected one enzyme for structural studies, and here report the ... The closest homologous structures currently available are 4KNA (N-succinylglutamate 5-semialdehyde dehydrogenase from Burkholderia thailandensis) and 3JU8, with amino acid sequence identity of 63% and 62% respectively. ...
775 3tmg - Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha-and Gammaproteobacteria 2017 J Herrou, JW Willett, DM Czy, G Babnigg - Journal of , 2017 - Am Soc Microbiol ... meliloti ChoX (PDB IDs 2REG and 2RIN) (37, 38) and EhuB (PDB ID 2Q88) (39), E. coli ProX(PDB IDs 1R9L and 1R9Q) (40), and Borrelia burgdorferi ProX (PDB ID 3TMG). ... Residue numberingstarts with the first residue present in the corresponding structure in the PDB. ...
776 4weo - Rational design of Meso2, 3butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations 2017 Z Pu, F Ji, J Wang, Y Zhang, W Sun, Y Bao- Febs Letters, 2017 - Wiley Online Library Sequence and structure alignment of the four BDHs. (A) Structure superposition of the BDHs in Protein Data Bank ( PDB code 1GEG: cyan; 3A28: green; 3WYE: yellow; 4WEO : red). (B) Sequence alignment between the four BDHs
777 4kgn - Structural and Biochemical Insights into the 2O Methylation of Pyrimidines 34 in tRNA 2017 P Pang, X Deng, Z Wang, W Xie - The FEBS Journal, 2017 - Wiley Online Library ...Figure 4. The structure and sequence comparison with orthologs from other organisms. (A) Structure overlay of the polypeptide-chain backbones in cross-eyed stereo view (represented as Cα traces) of TtTrmL (green), apo Yibk (cyan, PDB code 4KDZ), EcTrmL (magenta, PDB code 4JAK), Apo HiTrmL (yellow, PDB code 1J85), HiTrmL in complex with SAH (pink, PDB code 1MXI), Burkholderia pseudomallei TrmL in complex with SAH (gray, PDB code 4KGN). ...
778 4wec - Binding of NADP+ triggers an open-to-closed transition in a mycobacterial FabG -ketoacyl-ACP reductase 2017 M Blaise, N Van Wyk, F Banres-Roquet - Biochemical , 2017 - biochemj.org ... A BLAST analysis using the MSMEG_6753 primary sequence to query the protein databank shows that the crystal structures of Ralstonia sp. alcohol dehydrogenase [24] (PDB:4BMS), Bacillus subtilis FabG [18] (PDB:4NBU) and the uncharacterized SDR MSMEG_2598 (PDB:4WEC) from M. smegmatis (unpublished) possess the highest scores, sharing 42, 37 and 37% primary sequence identity with MSMEG_6753, respectively ...
779 3sbx - A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis 2017 R Bhagavat, HB Kim, CY Kim, TC Terwilliger- Scientific reports, 2017 - nature.com a given ligand recognition, and (d) sensitive methods are required to compare structural motifs against binding sites 33 and combine them into a workflow to obtain structure -based function a large-scale analysis of 4,766 ATP and other NTP binding proteins from PDB and have
780 5eln 4efi, 3q1t Self-association of a highly charged arginine-rich cell-penetrating peptide 2017 G Tesei, M Vazdar, MR Jensen- Proceedings of the, 2017 - National Acad Sciences ionic strengths, owing to an interaction mode which is present in the structure of a MD simulations elucidate the origin of the R10R10 attraction by providing structural information on in biological systems by inspection of protein crystal structures in the Protein Data Bank ( PDB )
781 4weo - Rational design of Meso2,3butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations 2017 Z Pu, F Ji, J Wang, Y Zhang, W Sun, Y Bao- FEBS letters, 2017 - Wiley Online Library (A) Structure superposition of the BDHs in Protein Data Bank ( PDB code 1GEG: cyan; 3A28: green; 3WYE: yellow; 4WEO : red). (B) Sequence alignment between the four BDHs. It was prepared with the program Espript 3.0 (http://espript.ibcp.fr)
782 3gmt - Exploring protein dynamics using graph theory and single-molecule spectroscopy 2017 R Peach - 2017 - spiral.imperial.ac.uk 4.1 Weighted graph construction from an experimental PDB structure The increased understanding between structure , dynamics and function offers opportunities for protein ... Despite the myriad of structures, only four are available in the apo state (PDB ID: 4AKE, 2RH5, 3UMF and 3GMT) which takes the form of the open conformation.
783 3slg - Applying structural enzymology to understand the reactivity of different biocatalysts 2017 C Binda - iris.unipv.it Structural biology applied to enzymes allows to describe in detail the architecture of their active sites and uncover the This method necessarily can be applied when the structure of a protein homologous to the target one is already available (ie present in the PDB database or
784 4gl8 - INVESTIGATION OF THE LIPOPROTEOME OF THE LYME DISEASE BACTERIUM BORRELIA BURGDORFERI 2017 AS Dowdell - 2017 - kuscholarworks.ku.edu lipoproteins, such as OspA (88, 89). Structural analysis of Lp6.6 showed that it exists primarily in aggregation-prone -helices and disordered stretches, and it is hypothesized that its unconstrained tertiary structure may be important for its biological role (90). Another similarly
785 5eo6 4exq, 4wsh Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product 2017 A Bailey, R Webster, R Hunter, N Freemantle, G Rait - 2017 - Microbiol Mol Biol Rev The crystal structure of the P. aeruginosa enzyme shows that it is composed of Interestingly, crystal structures of P. aeruginosa variants with cysteine substitutions show decreasing Although structural information on porphobilinogen synthases from many sources shows that the
786 4ijn - Acetate Metabolism: The physiological role of ADP-forming acetyl-CoA synthetase and acetate kinase in Entamoeba histolytica 2017 T Dang - 2017 - tigerprints.clemson.edu ... these predictions. Inhibition and structural activity relationship studies revealed an ... 1.6 Acetate producing pathways within E. histolytica.....26 1.7 The structure of Methanosarcina thermophila acetate kinase.....30 ...
787 4lfy - Targeting Pyrimidine Pathway of Plasmodium knowlesi: New Strategies Towards Identification of Novel Antimalarial Chemotherapeutic Agents 2017 M Rashmi, MK Yadav, D Swati- Combinatorial chemistry & high, 2017 - ingentaconnect.com The structural quality factors and overall Z-scores of simulated PkDHOase structure were found within the valid limits, and thus may be used for drug design purposes Organism Query Coverage (%) Identity (%) PDB ID Burkholderia cenocepacia J2315 96 32 4LFY
788 4o6r - Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway 2017 B Jia, X Jia, KH Kim, ZJ Pu, MS Kang, CO Jeon - Scientific Reports, 2017 - ncbi.nlm.nih.gov ... using the Modeller 9 program 28 based on the crystal structures of SALDpp (PDB ID: 4JZ6) andother aldehyde dehydrogenases (PDB ID: 4FR8, 4O6R, 4NMK, 2O2P, and ... The three-dimensionalstructure of SALDan was modeled using the Modeller 9 software program 28 . ...
789 3p10 3p0z, 3qhd, 3q8h, 3mbm L-Tryptophan hydroxamic acid derivatives as Burkholderia pseudomallei IspF inhibitors 2017 CA Muller - 2017 - commons.lib.niu.edu bank ( PDB ) file of the Burkholderia pseudomallei IspF crystal structure (3P0Z) was uploaded to AutoDock Tools. The water molecules were removed from the enzyme, as well as any co- crystallized structures (FOL955 and cytidine) and free ions (K+ and Cl-). This cleaned up
790 5vrb 3uk1, 3upt, 4xeu Ingnierie de la transctolase de Geobacillus stearothermophilus: nouvelles stratgies pour la synthse enzymatique de cetoses rares 2017 M Lorilliere - 2017 - tel.archives-ouvertes.fr Neisseria gonorrhoeae (2017) (5VRB.pdb) ou Chlamydomonas reinhardtii (2017) [76], toutes les TKs sont dimériques et constituées de deux sous-unités
791 4xi8 4lu4, 4n67, 4py3 Structure et fonction des toxines bactriennes domaine FIC 2017 S Veyron - 2017 - theses.fr proteins from Helicobacter pylori and Neisseria meningitidis, which were determined as part of Structural Genomics Initiatives in 2006 ( PDB entries 2G03 and 2F6S, which have no associated publications). However, the structure of FIC proteins only began to be discussed
792 4jnq - Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation 2017 MS Setzer, KG Byler, IV Ogungbe, WN Setzer - Scientia Pharmaceutica, 2017 - mdpi.com ... Page 8. Sci. Pharm. 2017, 85, 5 8 Figure 4. Overlay of the protein structures of Brucella melitensisTxR, PDB 4JNQ [24] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blueribbon). The co-crystallized ligand is shown as a wireframe structure. ...
793 3rih - Functional genetic variant of WW domain-containing oxidoreductase (WWOX) gene is associated with hepatocellular carcinoma risk 2017 HL Lee, HL Cheng, YF Liu, MC Chou, SF Yang - PloS one, 2017 - journals.plos.org ... Strick consensus amino acids in the putative active centers of compact structural units are shown: the key amino acids of active ... of human WWOX using the SWISSMODEL server based on M. abscessus short chain dehydrogenase or reductase crystal structure ( PDB ID: 3RIH ). ...
794 3uam - Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars 2017 KK Meier, SM Jones, T Kaper, H Hansson- Chemical, 2017 - ACS Publications Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide ... Table 4. AA10 LPMO Structures Available in the Protein Data Bank Burkholderia pseudomallei LPMO10A, BpAA10A 3UAM
795 3v7o - Ebola virus VP30 and nucleoprotein interactions modulate viral RNA synthesis 2017 W Xu, P Luthra, C Wu, J Batra, DW Leung- Nature, 2017 - ncbi.nlm.nih.gov ... resolution data crystal forms were solved by molecular replacement using the Reston virus VP30 structure ( PDB 3V7O ) as the ... Comparison of the eVP30 structure for residues 142266 between VP30-bound and -free show limited structural changes (Supplementary Fig ...
796 4ege - Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro 2017 VN Are, A Kumar, S Kumar, VD Goyal, B Ghosh - et Biophysica Acta (BBA , 2017 - Elsevier ... are lacking with literature reports of either only structural data (PDB entries; 1WN1, 1WY2, 3Q6D,2IW2, 4EGE) or only ... for this was prepared by Chainsaw [26] using the XPDxc protein sequenceand the structure of a putative XPD from Thermococcus sibiricus (PDB: 4FKC) [8 ...
797 3i3r - Structure-Based Targeting of Orthologous Pathogen Proteins Accelerates Antiparasitic Drug Discovery 2017 V Jain, A Sharma, G Singh, M Yogavel - ACS Infectious , 2017 - ACS Publications ... Structures for dihydrofolate reductase (DHFR) inhibitors pyrimethamine, methotrexate, and trimetrexate that are active against P. falciparum, T. brucei, and T. cruzi, respectively. (B) DHFR domain architectures and active site residues are similar in many pathogens: Trypanosoma cruzi (PDB: 3HBB), Cryptosporidium hominis (PDB: 1QZF), Trypanosoma brucei (PDB: 3QFX), Babesia bovis (PDB: 3I3R),. ...
798 4pca 4oa5, 4oa8 Outer Membrane Protein OmpB Methylation May Mediate Bacterial Virulence 2017 DCH Yang, AH Abeykoon, BE Choi, WM Ching- Trends in Biochemical, 2017 - Elsevier ... on methylation of bacterial OMPs has uncovered novel mechanisms with respect to protein structure and catalytic ... of the 226-residue dimeric O-methyltransferase have been determined in its apo form ( PDB ID:4OA8) and in complex with AdoMet (4OA5) or AdoHcy ( 4PCA ). ...
799 4xxp - Placeholder factors in ribosome biogenesis: please, pave my way 2017 FJ Espinar-Marchena, R Babiano, J Cruz - Microbial Cell, 2017 - ncbi.nlm.nih.gov ... As expected from this structural similarity, cryo-EM and CRAC analyses confirmed that Tsr1 binds,albeit differently than ... MDM2 fragment was taken from 4XXP 164 after superimposing the structure shown in this file with that of L11 shown in A. ...
800 4lgv - Substrate Channeling in an Artificial Metabolon: A Molecular Dynamics Blueprint for an Experimental Peptide Bridge 2017 Y Liu, DP Hickey, JY Guo, E Earl, S Abdellaoui - ACS , 2017 - ACS Publications Figure 3. (A) Illustration of the proposed channeling complex using a poly(lysine) bridge as an electrostatic surface between hexokinase (HK; PDB 3VF6) and glucose-6-phosphate dehydrogenase (G6PDH; PDB 4LGV).
801 5ids - Mrub_2052, Mrub_0628, and Mrub_2034 genes are predicted to be orthologous to b0688, b2039, and b3789 genes found in Escherichia coli, which are involved in 2017 JP Hartnett, D Scott - 2017 - digitalcommons.augustana.edu ... (Finn et al.). Protein Data Bank ( PDB ) (Berman et. al., 2000) is a curated collection of crystalized proteins.If a PDB hit is obtained for a query sequence, then 3-D structure neighbors, Page 7. 6 ... PDB protein database 5IDS Glucose-1-phosphate Thymidylyltransferase ...
802 3uam - The discovery of novel LPMO families with a new Hidden Markov model 2017 GP Voshol, E Vijgenboom - BMC Research , 2017 - bmcresnotes.biomedcentral.com ... Q3JY22. 3UAM. nd. nd. AA10 (formerly CBM33). ... The structure of one of the AA10 LPMOs fromStreptomyces coelicolor A3(2) (PDB ID: 4OY7) [39], with the copper atom shown as a sphereand highly conserved residues labeled and shown as sticks. Genome mining for LPMOs. ...
803 3meq - Adaptations to high salt in a halophilic protist: differential expression and gene acquisitions through duplications and gene transfers 2017 T Harding, AJ Roger, AGB Simpson- Frontiers in microbiology, 2017 - frontiersin.org WP_041596283.1), and sequences for characterized NADPH-dependent enzymes from S. cerevisiae (1Q1N), P. perezi (1P0C), Helicobacter pylori (3TWO), Populus tremuloides (1YQD) and Catharanthus roseus (5H81), and for NADH-dependent enzymes from Moraxella sp. (4Z6K), Geobacillus stearothermophilus (3PII), Ralstonia eutropha (3S1L), Brucella suis (3MEQ), and Pseudomonas aeruginosa (1LLU). (B) Maximum-likelihood phylogenetic tree for zinc-dependent alcohol dehydrogenase showing strongly supported clustering (gray
804 3qxz 3rsi, 3pk0, 5b8i, 5ji5, 4qfe, 3moy Human Missense Variation is Constrained by Domain Structure and 2017 SA MacGowan, F Madeira, T Britto-Borges - discovery.dundee.ac.uk the protein structure level. Figure 2B shows that this result extends to other protein 109 For 182 an example see Glu 295 and Ser 332 in PDB ID: 3e00 chain D.).21 These important 183 Glu370 that recent structural studies suggest is at the interface with Ubiquitin22 and so 187
805 3mqd - Exploring Protein Structure: Seeing the Forest and the Trees 2017 AE Brereton - 2017 - ir.library.oregonstate.edu Experimental Methods to Obtain Structures Only a few experimental methods exist that can yield enough information to accurately determine the 3-dimensional structure of a folded protein complete structural information often comes from using a combination of the methods
806 3ek2 - Crystalline Structure of FABI from Burkholderia Pseudomallei 2017 NR Krishnamurthy - US Patent , 2017 - freepatentsonline.com ... Analysis of X-Ray Structure of BpmFabI. ... The structural superposition showed an rms deviationof 1.047 , 0.87 and 1.07 respectively for Bpm (256 Ca atoms; PDB; 3EK2), Ec (251 Caatoms; PDB; 4JQC) and ScFabI (242 Ca atoms; PDB; 4FS3) crystal structures. ...
807 3v8h - Inactivation of the thymidylate synthase thyA in non-typeable Haemophilus influenzae modulates antibiotic resistance and has a strong impact on its interplay 2017 I Rodrguez-Arce, S Mart, B Euba- Frontiers in cellular, 2017 - frontiersin.org Antibacterial treatment with cotrimoxazol (TxS), a combination of trimethoprim and sulfamethoxazole, generates resistance by, among others, acquisition of thymidine auxotrophy associated with mutations in the thymidylate synthase gene thyA, which can modify the biology A prediction of ThyAH. influenzae tertiary structure, based on Burkholderia thailandensis ThyA protein (PDB: 3V8H), was generated by the automated modeling tool of the Swiss Model web service
808 4dz6 - How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions ( 2017 GM Blackburn, J Cherfils, GP Moss - Pure and Applied , 2017 - degruyter.com ... For the nucleoside-diphosphate kinase from B. burgdorferi, a vanadate transition state complex links ADP and His 134 as axial ligands (PDB entry 4DZ6). There is no catalytic metal to coordinate the three equatorial oxygen atoms. ...
809 4zju - A Novel Series of Enoyl Reductase Inhibitors Targeting the ESKAPE Pathogens, Staphylococcus aureus and Acinetobacter baumannii 2017 J Kwon, T Mistry, J Ren, ME Johnson- Bioorganic & Medicinal, 2017 - Elsevier and AbFabI. These enzymes share a high sequence identity (45% identity) and structural similarity (RMSD for all residues < 1 when the various crystal structures of SaFabI are overlaid with the crystal structure of AbFabI). As a
810 4mpq - Structural Characterisation of members of the DHDPS/NAL subfamily of proteins 2017 C MacDonald - 2017 - ir.canterbury.ac.nz 2HMC A. tumefaciens HypD 4MPQ B. melitensis HypD p(r) Pair distribution function plot pdb Protein data base This information is displayed using espript software (Robert and Gouet 2014) with secondary structure of E. coli DHDPS being shown along the top
811 5i1f - Structure of the Bacillus anthracis dTDP-l-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA) 2017 J Baumgartner, J Lee, AS Halavaty- Section F: Structural, 2017 - scripts.iucr.org The Mg2+ ion is modeled from the RffH structure The GalU homologs are from Burkholderia vietnamiensis ( PDB entry 5i1f ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Sphingomonas elodea ( PDB entry 2ux8), respectively
812 4jgb 4jga Targeting Transforming Growth Factor Beta-Activated Kinase 1 as a Therapeutic 2017 J Totzke - 2017 - dukespace.lib.duke.edu 50 3.4 Structural and functional similarities between TAK1 and related kinases ..... 50 Page 8. viii 4 Figure 2: Crystal structure TAK1 ( PDB 5V5N, left ribbon, right hydrophobicity surface) .... 11
813 4w91 - Ironsulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding 2017 J Prard, SO de Choudens- JBIC Journal of Biological Inorganic, 2017 - Springer Structural and biophysical analyses of Suf proteins SufS There are five crystal structures of SufS protein ( PDB numbers: 5J8Q; 4W91 ; 1T3I; 5DB5; 1I29) whose three published (Fig. 4) [7173]. The first crystal structure was Fig. 4 Overview of Suf protein structures SufS 1I29
814 2n6x - RNA structure refinement using NMR solvent accessibility data 2017 C Hartlmller, JC Gnther, AC Wolter, J Whnert - Scientific , 2017 - ncbi.nlm.nih.gov ... Figure 4b ) and the corresponding sPRE values are underestimated based on the NMR solution structure , independent of which structural model of the UUCG loop motif ( PDB codes 1HLX, 1K2G, 1TLR, 1Z31, 2KHY, 2KOC, 2KZL, 2LHP, 2LUB and 2N6X ) was used. ...
815 4djt - Existuj sekvenn determinanty funkn divergence GTPz? 2017 O Kraus - 2017 - dspace.cuni.cz ... responsible for major functional differences between different protein families. To compare them,I have used the structural data from the PDB database and sequences from the UniProt database. ...protein structure on the example of small GTPases. The first results are not ...
816 3sdo - Crystal structure of dibenzothiophene sulfone monooxygenase BdsA from Bacillus subtilis WUS2B 2017 M Okai, WC Lee, LJ Guan, T Ohshiro - Proteins: Structure, , 2017 - Wiley Online Library ... Overall structure. ... BdsA also shows structural similarities with the following proteins: putativemonooxygenase Ytnj (PDB ID: 1TVL; Q-score 0.60, not published), nitrilotriacetatemonooxygenase NmoA (PDB ID: 3SDO; Q-score 0.57, not published), EDTA monooxygenase ...
817 3h81 - Molecular insight into the acryloyl-CoA hydration by AcuH for acrylate detoxification in dimethylsulfoniopropionate-catabolizing bacteria 2017 HY Cao, P Wang, F Xu, PY Li, BB Xie, QL Qin- Frontiers in, 2017 - frontiersin.org Structure Determination and Refinement. The structure of RdAcuH was solved by molecular replacement using Phaser (Potterton et al., 2003). An enoyl-CoA hydratase ( PDB ID code: 3H81 ) was used as the searching model
818 5hxa - Cloning and expression analysis of tps, and cryopreservation research of trehalose from Antarctic strain Pseudozyma sp. 2017 H Yin, Y Wang, Y He, L Xing, X Zhang, S Wang, X Qi- 3 Biotech, 2017 - Springer of NJ7 was similar to the alpha, alpha-trehalose-phosphate synthase of 5hxa .1 (Mayclin were drawn into ten frames, which played important roles in maintaining the structure and function It can also act as a sensing compound, growth regulator and structural component of cell
819 2n6t 2n6s, 2n6x, 2n6w F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly 2017 S Jain, T Schlick- Journal of molecular biology, 2017 - Elsevier Table 1. List of 50 RNA PDB files whose 3D structures were generated in this paper. PDB , Residues, Molecule, Structure . 2M4W, 17, HEV genome bulge, Hairpin, internal loop 2N6T , 42, CssA mRNA thermometer top, Hairpin, internal loops
820 3h81 - Genomics-based discovery and engineering of biocatalysts for conversion of amines 2017 MM Heberling, CP Postema, TJ Meijer, M Otzen - rug.nl peptides and macrolactam polyketides through de novo biosynthesis [1,2]. The structural diversity and The structure of -Val (or other dialkylglycines) restricts the diversity of feasible ID) and an enoyl-CoA hydratase from Mycobacterium tuberculosis ( PDB : 3H81 , 62%), as seen
821 4ex4 - Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa 2017 AC McVey, P Medarametla, X Chee, S Bartlett- Biochemistry, 2017 - ACS Publications ... G. Inactivation of these enzymes has been reported to abolish the ability of P. aeruginosa to establish infection in a mammalian model system, yet we still lack the structural information to support drug design efforts. In this work, we describe the first X-ray crystal structure of P ...
822 3gmt - Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins 2017 SL Seyler - 2017 - search.proquest.com The intricacies of the current state of knowledge surrounding protein conformational. transitions and the structure -function connection is perhaps more easily understood in the and four in ligand-free (apo), open-like states ( PDB IDs 4ake, 2rh5, 3umf, 3gmt [26])
823 2kn9 - Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry 2017 BK Maiti, RM Almeida, I Moura, JJG Moura- Coordination Chemistry, 2017 - Elsevier Rubredoxins (Rds) and their derivatives have been extensively used, in the last few decades, in order to elucidate structure and functional aspects of metal sit.
824 3kc6 - Inhibition of Avian Influenza A Virus Replication in Human Cells by Host Restriction Factor TUFM Is Correlated with Autophagy 2017 SM Kuo, CJ Chen, SC Chang, TJ Liu, YH Chen - mBio, 2017 - Am Soc Microbiol ... (B) Modeling of the A/Anhui/1/2013(H7N9) virus PB2 CTD based on the A/Vietnam/1203/2004( H5N1) virus ( PDB ID 3KC6 ). ... as GTP-binding D1), and thus, the lack of association between chTUFM and PB2 627 E may be due to these in sequence and structure differences in ...
825 4f2n 3js4 Anion interactions in active centers of superoxide dismutases 2017 VR Ribi, S Stojanovi, MV Zlatovi- International Journal of Biological, 2017 - Elsevier ... 2rcv, 2w7w, 3ak2, 3ce1, 3dc6, 3evk, 3f7l, 3h1s, 3js4, 3lio, 3lsu, 3mds, 3pu7, 3tqj, 4br6, 4c7u, 4f2n , 4ffk, 4yet ... For example, in the crystal structure of superoxide dismutase (Fe) (sodB) from Coxiella burnetii ( PDB ID: 3tqj), there exists a anion interaction structure motif (Fig ...
826 3uam - Structural Dynamics of Lytic PolysaccHaride Monooxygenase 2017 P Bharval, S Sarswati, RM Yennamalli - 2017 - 122.252.232.85 (a) For AA9 the reference structure is 2bem, (b)For AA10 the reference structure is 2bem (c) For AA11 the reference structure is 4MAH PDB ID RMSD 2BEN 0.303 2LHS 1.273 2XWX 0.491 2YOW 0.445 2YOX 0.474 2YOY 0.440 3UAM 0.700 4A02 0.880 4ALC 0.673
827 3mqd - Exploring Protein Structure: Seeing the Forest and the Trees. 2017 AE Brereton - 2017 - ir.library.oregonstate.edu Experimental Methods to Obtain Structures Only a few experimental methods exist that can yield enough information to accurately determine the 3-dimensional structure of a folded protein complete structural information often comes from using a combination of the methods
828 4lc3 - Structural and functional characterization of a unique hypothetical protein (WP_003901628. 1) of Mycobacterium tuberculosis: a computational approach 2017 R Uddin, S Rafi- Medicinal Chemistry Research, 2017 - Springer ... 2011). Table 8 RMSD of top Z-ranked ProBis ligands after docking with modeled structure . S.No. PDB ID. 1 st ranked RMSD (). Lowest RMSD (). 1. 1O69. 4.93. 3.45. 2. 1MDO. 3.02. 2.89. 3. 2C81. 6.43. 3.9. 4. ... 8. 3UWC. 3.37. 3.36. 9. 4K2M. 9.68. 2.5. 10. 4LC3 . 8.24. 3.91. 11. 1B9H ...
829 3meb 4f4f, 4otl Bioinformatic and Biophysical Analyses of Proteins 2017 J Catazaro - 2017 - digitalcommons.unl.edu structure of every protein encoded within a particular genome, the aim is to concentrate to steadily produce structural representatives of previously uncharacterized genes. Although the new structures have been deposited in the Protein Data Bank ( PDB ) 4
830 3ek2 - Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase 2017 C Neckles, S Eltschkner, JE Cummings - Biochemistry, 2017 - ACS Publications ... Structural analysis of nine enzyme:inhibitor complexes reveals that the variation in structure kinetic relationships can be rationalized by structural rearrangements of bpFabI1 and subtle changes to the orientation of the inhibitor in the binding pocket. ...
831 3iml 3dms, 3hja, 3gtd, 3mbf, 3sth, 3s82, 3qbp, 3l0d, 3kx6, 4oh7, 4xfj, 4tu1 Investigation of intrinsic dynamics of enzymes involved in metabolic pathways using coarse-grained normal mode analysis 2017 SM Meeuwsen, AN Hodac, LM Adams - Cogent , 2017 - Taylor & Francis ... (3IML), and M. avium (3S82) MATs together. The dynamics of 3IML are more similar to the ... 6) toassist in the open and closed conformations of the enzyme. Ornithine transcarbamylase (PDBcode: 4OH7; chains A and B of the homotrimer were ... Visualization of the structure ...
832 3nrr - Pharmacoinformatic Study on the Selective Inhibition of the Protozoan Dihydrofolate Reductase Enzymes 2017 VK Sharma, S Abbat, PV Bharatam - Molecular Informatics, 2017 - Wiley Online Library ... The three dimensional crystal structure with PDB IDs, 3INV for AdDHFR (48.82%), HmmDHFR (50.24 ... 50.72 %), LdDHFR (50.49 %), and LmDHFR (50.98%), 4EIL for TtDHFR (37.57%), 3NRR for BgDHFR ... drug design process.[46] It was observed that the 3D structure of the ...
833 3uw1 4em8, 3u7j Identificao in silico de potenciais inibidores da ribose 5-fosfato isomerase de Trypanosoma cruzi 2017 VVS Castilho - 2017 - arca.fiocruz.br In this study, novel potential inhibitors were proposed for the Rpi of T. cruzi (TcRpi) based on a computer-aided approach, including structure -based and ligand-based pharmacophore modeling ativo da estrutura cristalogrfica TcRpiB ( PDB 3K7S) .... 70
834 4dyw 3hhj The evolution of function within the Nudix homology clan 2017 JR Srouji, A Xu, A Park, JF Kirsch- Proteins: Structure,, 2017 - Wiley Online Library ... Despite the structural similarity, sequence identity within the Nudix homology domain between these ... and X is any amino acid) constitutes a loop-helix-loop structure that is ... diphosphate isomerase family (represented by E. coli isopentenyl diphosphate isomerase PDB ID: 1NFS ...
835 4mei 4jf8, 4lso, 4kz1, 4o3v, 4nhf Structural and Molecular Biology of Type IV Secretion Systems 2017 L Terradot, C Berg, G Waksman- Type IV Secretion in Gram-Negative, 2017 - Springer 1.2 Composition of T4SSs. X-ray crystallography, nuclear magnetic resonance (NMR), and more recently electron microscopy have been successfully used to provide insights into the structure of T4SSs Plasmid or bacteria. PDB or EMDB ID 4KZ1,4JF8,4LSO, 4MEI ,4NHF m
836 3qh8 3sbx Deciphering common recognition principles of nucleoside mono/di and triphosphates binding in diverse proteins via structural matching of their binding sites 2017 R Bhagavat, N Srinivasan- Proteins: Structure, 2017 - Wiley Online Library One highest resolution structure was taken as the representative for each site architecture or BScID type Site type (ST), Representative PDB code, Cluster size, No ST19, 3T7M, 6, 6, L80 [0.86], D102, V82, T8 [0.71], LI/TR/OX/HY. ST20, 3QH8 , 6, 6, H86 [0.71], H219, D188, S18 [0.57
837 2lbb - Lipid membranes and acyl-CoA esters promote opposing effects on acyl-CoA binding protein structure and stability 2017 MC Micheletto, LFS Mendes, LGM Basso - International Journal of , 2017 - Elsevier ... Other secondary structures such as loops and disordered conformations contribute to the remaining 37%, whose values are consistent with the available structures of ACBP homologues in the protein data bank (PDB ID 2ABD, 3FP5 and 2LBB). Incubation with OCoA does not change the CD spectrum of CnACBP...
838 3rr2 - Structural characterization and functional analysis of cystathionine synthase: an enzyme involved in the reverse transsulfuration pathway of Bacillus anthracis 2017 S Devi, A Rehman, A Syed, KF Tarique- The FEBS, 2017 - Wiley Online Library Superposition of the BaCBS structure (purple) with the (A) human CBS ( PDB ID: 1M54), (B) PLP-bound OASS ( PDB ID: 2Q3B), and (C) PLP-unbound OASS ( PDB ID: 1O58) structures . (D) Structural superposition of BaCBS (purple) with PDB ID: 1OAS (yellow), PDB ID: 1VE1
839 3uam - Lytic polysaccharide monooxygenases from Myceliophthora thermophila C1 2017 M Frommhagen - 2017 - library.wur.nl Furthermore, many more variations exist in the xylan structure , such as ester-linked ferulic and p-coumaric acid substitutions than can be further crosslinked to lignin (Section Structures are modified and based on Scheller et al Structural units are shown in the legend on the top ..Table 1.3 Crystal structures of AA9 and AA10 LPMOs published until the end of 2013. CBM33 3UAM Burkholderia pseudomallei AA10 2011 SSGCID
840 3sbx - Structural basis for a novel type of cytokinin-activating protein 2017 H Seo, KJ Kim - Scientific Reports, 2017 - ncbi.nlm.nih.gov ... M. marinum (MmLOG) in complex with AMP (Protein Data Bank code 3SBX) revealed the ... Therefined model of CgLOGII was deposited in the Protein Data Bank (PDB code 5WQ3 ... Thethree-dimensional structure of Lonely Guy from Claviceps purpurea provides insights into the ...
841 4g7f - Insights into the Giardia intestinalis enolase and human plasminogen interaction 2017 R Aguayo-Ortiz, P Meza-Cervantez, R Castillo- Molecular, 2017 - pubs.rsc.org ... P-BLAST analysis showed that T. brucei brucei ( PDB ID: 2PU1) and T. cruzi ( PDB ID: 4G7F ) exhibited the highest ... (B) Sequence alignment of the proposed HsPLG binding sites (highlighted in orange boxes) in the different organisms, (C) 3D structure superposition and ...
842 5dvw - Evolutionary Trends in Viral Pathogens within and between Outbreaks 2017 ME Saha - 2017 - etd.ohiolink.edu for VP35 the 3FKE and 4YPI maps were used. For the other VP proteins: maps 4LDD and 4LDB for VP40, maps 2I8B and 5DVW
843 3i4e -