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 3cez - 1 H, 13 C and 15 N resonance assignment of a zinc-binding methionine sulfoxide reductase type-B from the thermophilic archeabacterium Methanothermobacter thermoautotrophicus 2010 M Carella, O Ohlenschl?ger, R Ramachandran? - Biomolecular NMR Assignments, 2010 - Springer ... 2) as predicted from chemical shifts by using TALOS+ (Shen et al. 2009) are in close agreement with the ones present in other known MSRB structures (eg PDB 3HCJ, 3CEZ, 1L1D). The 13Ca and 13Cb chemical shifts suggested (Kornhaber et al. ...
2 3l56 - 3D Molecular Modelling Study of the H7N9 RNA-Dependent RNA Polymerase as an Emerging Pharmacological Target 2013 D Vlachakis, A Karozou, S Kossida - Influenza research and treatment, 2013 - hindawi.com ... The sequence alignment and the blastp query that followed revealed that the PA domain was available in the PDB databank. ... entry: 4ENF), and the crystal structure of the large C-terminal domain of the polymerase basic protein 2 from influenza A virus (RCSB entry: 3L56). ...
3 3khw - 3D protein structure prediction of influenza A virus based on optimization genetic algorithm. 2014 J Gao, PX Jin, HX Xu - Pakistan journal of pharmaceutical sciences, 2014 - pjps.pk ... acid residues Sixty groups of influenza A (H1N1) virus protein were selected from PDB database, 3HTO, 4F15, 3B7E, 3BEQ, 3HTP, 3HTQ, 3HTT, 4EDB, 4B7N, 4B7M, 3M5R, 3M8A, 3LKN, 3QQ4, 3QQ3, 3TI3, 3LZF, 3M6S, 3UBE, 3UBJ, 3UBN-A, 4D9J, 3GBN, 3KHW, 4EDA, 2ZKO ...
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 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
6 3eom 3pfd, 3swo, 4n5f 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA … 2015 M Schürmann, R Meijers, TR Schneider… - … Section D: Biological …, 2015 - scripts.iucr.org ... (2011). Acta Cryst. D67, 235-242.] ) with the crystal structure of an acyl-CoAdehydrogenase from Thermus thermophilus HB8 (PDB entry 1ukw ; RIKEN StructuralGenomics/Proteomics Initiative, unpublished work) as the search model. ...
7 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).
8 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
9 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
10 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
11 3eoo - Accelerating knowledge-based energy evaluation in protein structure modeling with Graphics Processing Units 2012 A Yaseen, Y Li - Journal of Parallel and Distributed Computing, 2011 - Elsevier ... PDB #of Res #of Atoms GPU Time L1 hits L1 misses Divergent Branches Sorted (??sec) Unsorted (??sec) Sorted/ Unsorted Sorted Unsorted Sorted Unsorted Sorted Unsorted 1PRB 53 419 49 76 ... 1.05 6,88 5 ,7 80 3,83 9 ,5 00 36 4, 04 8 66 6, 21 7 17 9, 78 4 33 ,5 41 3EOO 4,59 ...
12 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
13 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
14 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 ...
15 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
16 3dmo - Achievements of structural genomics 2011 TC Terwilliger - 2011 - permalink.lanl.gov ... Semi-automated Structure determination ~ ... PDB 3BV6, 2275 AA Metallo protein - ... l University ofIowa 2 University of Michigan Medical School Crystal structures of the FDTS-FAD- 3The JointCenter for Structural Genomics at GNF 4SSRL, Stanford University dUMP complex. ...
17 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.
18 3sdo - A Comprehensive Computational Analysis of Mycobacterium Genomes Pinpoints the Genes Co-occurring with YczE, a Membrane Protein Coding Gene 2017 T Milano, S Angelaccio, A Tramonti, ML di Salvo- Interdisciplinary, 2017 - Springer Clustal Omega multiple sequence alignment between the “luciferase-like” cluster sequences and a set of PDB structures detected by Phyre2 and/or HHpred. Sequence ids refer to Table 3 while PDB codes indicate: 3SDO|A, the chain A of nitrilotriacetate monooxygenase from Burkholderia pseudomallei
19 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
20 3ek1 3i44 A computational integrating kinetic study on the flexible active site of human acetaldehyde dehydrogenase 1 2016 Y Xu, J Lee, HS Yang, ZR L, H Mu, JM Yang - Process , 2016 - Elsevier ... In the first step, binding pocket residues were calculated based on the 3D structure of ALDH1via the Pck pocket ... We found 25 template PDB structures (1a4s, 1bxs, 1euh, 1o04, 1t90, 1uxt,1uzb, 1wnd, 2d4e, 2imp, 2j6l, 2o2p, 2ve5, 2w8n, 3b4w, 3ed6, 3ek1, 3i44, 3ifg, 3jz4 ...
21 3tmg - A conserved ABC transport system regulated by the general stress response pathways of Alpha-and Gammaproteobacteria 2016 J Herrou, JW Willett, DM Czy, G Babnigg - Journal of , 2016 - Am Soc Microbiol ... We included sequences of class I PBPs which have been co-crystallized with betaine-related ligands in our analysis, including: Archaeoglobus fulgidus ProX (PDB IDs: 1SW1, 1SW2, 1SW4 ... 1R9Q) (56), and Borrelia burgdorferi ProX (PDB ID: 3TMG) ...
22 3r7k - A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket 2015 AF Chai, EMM Bulloch, GL Evans, JS Lott… - Acta Cryst. (2015). D71, 862-872 …, 2015 - journals.iucr.org ... 2.10.0. Cambridge: Global Phasing Ltd.] ) alternating with manual rebuilding of the molecularstructure using Coot ... Protein, PDB code, C9-N10-N5-C4 (°), Distortion (°), Reference. ... Acyl-CoAdehydrogenase, 3r7k, 157.7, 22.3, Seattle Structural Genomics Center for Infectious Disease ...
23 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;
24 4gie - Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions 2017 V Swaminathan, JM Kalappurakkal- Proceedings of the, 2017 - National Acad Sciences ... How could transmembrane receptors sense directional force? Cytoskeletal forces are thought to provide an ultrasensitive mechanism for triggering integrin activation by inducing structural transitions between inactive and active integrin conformations (11). ...
25 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
26 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
27 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
28 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
29 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
30 2kwl 2l4b, 2l3v Acyl carrier protein structural classification and normal mode analysis 2012 DC Cantu, MJ Forrester, K Charov, PJ Reilly - Protein Science, 2012 - Wiley Online Library ... the amino acid residues between two structures compared for calculations; PDB: Protein Data Bank; PKS: polyketide synthase; RMSD: root mean square deviation; ThYme: Thioester active ... Protein Data Bank (PDB) ACP1 structures 1T8K, 1X3O, 2EHS, 2EHT, and 2QNW, ACP5 ...
31 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
32 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)
33 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.
34 3gmt - Adenylate kinase from< i> Streptococcus pneumoniae</i> is essential for growth through its catalytic activity 2014 TT Thach, TT Luong, S Lee, DK Rhee - FEBS Open Bio, 2014 - Elsevier ... Open, ligand-free SpAdK structure was solved by molecular replacement using PHENIX [35] with AdK from Marinibacillus marinus (PDB ID: 3FB4) and Burkholderia pseudomallei (PDB ID: 3GMT) as search models. ...
35 3laa - A domain dictionary of trimeric autotransporter adhesins 2014 J Bassler, BH Alvarez, MD Hartmann… - International Journal of …, 2014 - Elsevier ... Name, Description, Topological crossover, PDB. Anchor, Trimeric, 12-stranded outermembrane β-barrel, –, 2gr7. Stalk, Slender segment of predominantly coiled-coil structure, –, ...Long neck, Neck variant of 22 residues length, 120° cw, 3laa. ...
36 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
37 4di0 - Aerobic lineage of the oxidative stress response protein rubrerythrin emerged in an ancient microaerobic,(hyper) thermophilic environment 2016 JP Cardenas, R Quatrini, DS Holmes - Frontiers in Microbiology, 2016 - ncbi.nlm.nih.gov ... F9VPE5; PDB entry 1J30) and a rubrerythrin from Burkholderia pseudomallei (Uniprot accessionQ3JK2; PDB entry 4DI0) have three dimensional structures in the PDB. ... This difference in genecluster structure among members of the same phylum may be a reflection of the ...
38 3s4k - A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism 2017 A SnchezReyez, RA BatistaGarca - Proteins: Structure, , 2017 - Wiley Online Library ... All other parameters were set as default unless otherwise noted. Structure modelling by homology. ...In our first attempt to model ThYest_ar, I-TASSER[31] selected as templates from the PDB bacterial thioesterases (validated and putative): 1VH9 and 1VH5 (putative thioesterases from E. coli), 4K4C (thioesterase from E. coli), 1Q4T (thioesterase from Arthrobacter), 1SH8 (putative thioesterase from P. aeruginosa), 1SC0 (putative thioesterase from Haemophillus influenzae), 3S4K (putative esterase from ...
39 3ek2 - AFN‐1252 is a potent inhibitor of Enoyl‐ACP reductase from Burkholderia pseudomallei‐Crystal structure, Mode of action and biological activity 2015 KN Rao, A Lakshminarasimhan, S Joseph… - Protein …, 2015 - Wiley Online Library ... due to poor electron density. The structural models were generated using Pymol. 34 Summaryof ... The overall structure of BpmFabI in complex with AFN-1252 is similar to the earlier reportedapo-structure of Bpm FabI (PDB:3EK2) and ternary complex structures of Ec (E. coli: ...
40 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
41 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
42 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
43 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
44 4egf - A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis 2015 H Huang, MS Carter, MW Vetting - Journal of the , 2015 - ACS Publications ... 5) and (2) an experimentally verified l-xylulose reductase from M. smegmatis (MSMEG_3262;UniProt ID A0QXD6; PDB 4EGF) that shares 44 ... reaction that interconverts d-glyceraldhyde-3Pand dihydroxyacetone phosphate in glycolysis, ie, the active site structure can be ...
45 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
46 3hhe - A genomic signature and the identification of new sporulation genes 2013 AB Abecasis, M Serrano, R Alves, L Quintais… - Journal of Bacteriology, 2013 - Am Soc Microbiol Supplemental Material: B: structure based alignment between the YlzA protein and a putative ribose-5-phosphate isomerase from Bartonella henselae (pdb code 3HHE). Note that that the first 20 residues of YlzA do not align with the B. henselae protein.
47 3qat - A Hybrid NRPS-PKS Gene Cluster Related to the Bleomycin Family of Antitumor Antibiotics in Alteromonas macleodii Strains 2013 CM Mizuno, NE Kimes, M L?pez-P?rez, E Aus?? - PloS one, 2013 - dx.plos.org ... All-vs-all comparisons of the cluster sequences were performed using BLAST. Structural alignment of known protein structures of 1MLA, 3QAT, 2JFD and bleomycin family acyltransferase domains was performed using the PROMALS3D web server [32]. Phylogenetic analysis. ...
48 3uf8 - AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction 2015 D Xu, L Jaroszewski, Z Li, A Godzik - Bioinformatics, 2015 - Oxford Univ Press ... the first domain in SMT fusion Peptidyl-prolyl cis-trans isomerase (PDB ID 3uf8, chain A ... For example, the linker between the two domains in scFv-IL-1B complex (PDB ID 2kh2 ... for assembly of independently determined domains than for domains extracted from the structure of the ...
49 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)
50 3obk - Allostery and the dynamic oligomerization of porphobilinogen synthase 2012 EK Jaffe, SH Lawrence - Archives of biochemistry and biophysics, 2011 - Elsevier ... B) Subunits B, A and E (corresponding to subunits A,B and F of the oligomers illustrated in part A) of T. gondii PBGS (pdb: 3OBK) are shown as dark teal, gray and light teal cartoons with the remaining subunits of the 8mer shown as transparent white spheres. ...
51 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
52 3la9 3laa, 4lgo, 3s6l alpha/beta coiled coils 2016 MD Hartmann, CT Mendler, J Bassler, I Karamichali - eLife, 2016 - elifesciences.org ... 286 Given the structural identity between the -layers resulting from hexads and nonads in 287coiled coils, and the supersecondary structures we characterized at the transition between 288 ...systematically for other instances of -layers in proteins of known structure. ...
53 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
54 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
55 4o6r 4kna, 3i44, 3ek1 Amino acid residues that affect the basicity of the catalytic glutamate of the hydrolytic aldehyde dehydrogenases 2015 RA Muñoz-Clares, L González-Segura… - Chemico-Biological Interactions, 2015 - Elsevier ... groups as sticks with carbon atoms colored depending on the structure, oxygen in ... Family organism,enzyme (PDB code), pH crystal c, pK a, Hydrogen bond d ... Burkholderia cenocepacia, BCAM0469,AMP-complex (4O6R), 6.5, 7.42, Cys302↓ Gly270↓/Lys178↓ Glu399↑ Glu476 ...
56 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
57 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
58 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
59 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
60 2kok - AMPLIFICAO E CLONAGEM DO GENE draB de Azospirillum brasilense 2017 F Pinhelli - core.ac.uk melhor proteína-molde para o modelamento de DraB uma Arsenato redutase (arsC) de Brucella melitensis, cujo o número de acesso ao PDB é Bm-YffB ou 2kok. Elas possuem 23% de identidade,
61 4mow - Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase 2016 AM de las Heras - Microbial Cell , 2016 - microbialcellfactories.biomedcentral. ... Since the crystal structures of these AARs were not available, protein structures were made ... protein sequence identity to the C. necator AAR whose crystal structure was used ... Both S. wolfei homology models (Swol_0651 modelled on PDB: 4MOW [27] and Swol_1910 modelled ...
62 3dmo 3mpz Análise bioquímica, estrutural e funcional da enzima citidina deaminase (EC 3.5. 4.5) de Mycobacterium tuberculosis H37Rv 2014 ZAS Quitian - 2014 - meriva.pucrs.br ... This work presents the crystal structures of MtCDA in complex with uridine (2.4 Å resolution) and ...process, showing that structural flexibility of some residues are important to product binding. ... MtCDAstructure. The role of the conserved glutamate-47 (E47) residue was ...
63 3e5y - Analysis of coreperiphery organization in protein contact networks reveals groups of structurally and functionally critical residues 2015 AE Isaac, S Sinha - Journal of biosciences, 2015 - Springer ... residues are in the innermost cores, suggesting that the network core is critically important in maintaining the structural stability of ... 2.1 Protein structure analysis. ... set of 66 non-redundant protein structures obtained from the Protein Data Bank ( http://www.rcsb.org/pdb ) that include ... For the exceptions, viz., proteins with PDB ids 1a30, 1aac, 1auw, 1cbr, 1vl4, 3e5y and 3js3, we verified that those proteins among this group (
64 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
65 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
66 5b8f 3i3f, 3qxz Analysis of Pseudo-Symmetry in Protein Oligomers and its Correlation with Protein Dynamics 2017 K Shankar - 2017 - scholarworks.iupui.edu ... In fig.5.1, the protein with pdb code 1e9g is used to illustrate the structures generated to achievethe calculation. ... Fig. 5.2.: Structure Index in dimer 1e9g: Structural alignment of chain A with chainB generates A and chain B with A generates B. The difference between newly ...
67 3laa - Analysis of the BadA stalk from Bartonella henselae reveals domain‐specific and domain‐overlapping functions in the host cell infection process 2012 PO Kaiser, D Linke, H Schwarz, JC Leo… - Cellular …, 2012 - Wiley Online Library ... The structures are the YadA head (PDB ID: 1PH9) of Y. enterocolitica (Nummelin et al., 2004),the BpaA head ... structural motifs matches the colouring of the schematic diagram in A. The depictedstructural motifs of 3LAA occur in the inverse order in the original structure to that ...
68 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
69 5dd7 5cm7 Analysis of the Protein Binding Sites for Thiamin and Its Derivatives to Elucidate the Molecular Mechanisms of the Noncoenzyme Action of Thiamin (Vitamin B1) 2017 VI Bunik, VA Aleshin- Studies in Natural Products Chemistry, 2017 - Elsevier Elucidation of protein targets of the noncoenzyme thiamin action is advanced through structure -based identification of thiamin- or derivatives-binding protein patterns, bioinformatics analysis of their distribution among proteins and pathways, and experimental verification of the ... Active sites of the enzymes of thiamin metabolism. (A) Bacterial ThMP kinase with ThMP, nonhydrolyzable analog of ATP, and bound ions of magnesium (green) and potassium (purple) (PDB ID: 5DD7), the protein carbons in dark g
70 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).
71 3gvi - An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors 2016 P Laurino, Tth-Petrczy, R Meana-Paeda, W Lin - PLoS Biol, 2016 - journals.plos.org ... PDB (Protein Data Bank) IDs and corresponding cofactors: 1JG2, ADN; 3GVI, ADP; 2HMU, ATP;2XXB, AMP; 1BWC, FAD; 1V5E, FAD; 1EG2, MTA; 2A14, 2PBF ... A) Zoom-in view of the structureof L-3-hydroxyacyl-CoA dehydrogenase belonging to the Rossmann fold (PDB 1F17 ...
72 4wbs - An antibiotic binds to the ATPase that powers lipopolysaccharide transport 2016 JM May - 2016 - dash.harvard.edu This conclusion is supported by genetic, biochemical, and structural evidence, described below innermost layers of the cell envelope before turning our attention to the structure and assembly... though the C-terminus of E. coli LptB is not visible in the structures published by Sherman and collaborators, it is visible in the structure of Burkholderia phymatum LptB, crystallized with an N-terminal histidine tag in the absence of nucleotide (PDB: 4WBS)
73 3uf8 - An Approximated Voxel Approach for the Identification and Modelling of Ligand-Binding Sites 2012 LW Lee, A Bargiela - Journal of Physical Science and Application, 2012 - ico2s.org ... selected. These proteins are given as [PDB: 1FKF, 1BKF, 1YAT, 3VAW, 3UF8, 1C9H]. ... (a) (b) Fig. 14 (a) Screenshot of FK506-bound protein 3UF8 from the RCSB PDB with ligand site shown, (b) screenshot of the identified site from the voxel-based approximated method. ...
74 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.. ...
75 3d64 3n58 An enzyme captured in two conformational states: crystal structure of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii 2015 T Manszewski, K Singh, B Imiolczyk - Section D: Biological , 2015 - scripts.iucr.org ... pseudomallei (Seattle Structural Genomics Center for Infectious Disease, unpublished work,PDB entry 3d64 ), Brucella melitensis (unpublished work, PDB entry 3n58 ... Here, we present thefirst crystal structure of SAHase from a nodulating bacterium, Bradyrhizobium ...
76 2kok - A new arsenate reductase involved in arsenic detoxification in Anabaena sp. PCC7120 2013 S Pandey, AK Shrivastava, VK Singh, R Rai… - Functional & integrative …, 2013 - Springer ... b Structure-based multiple sequence alignment of All0195 homologs. ... 261278552
77 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
78 3k14 - An Extensive and Diverse Set of Molecular Overlays for the Validation of Pharmacophore Programs 2013 I Giangreco, DA Cosgrove? - Journal of chemical information and modeling, 2013 - ACS Publications ... All such algorithms must be validated with respect to known ligand overlays, usually by extracting ligand overlay sets from the Protein Data Bank (PDB). ... This is almost always done by reference to structures drawn from the Protein Data Bank (PDB). ...
79 3d64 3glq, 3n58 An Inexpensive Method for Selecting Receptor Structures for Virtual Screening 2015 Z Huang, CF Wong - Journal of chemical information and , 2015 - ACS Publications ... SPI also performed better than the best docking energy, the molecular volume of thebound ligand, and the resolution of crystal structure in selecting good receptorstructures for virtual screening. The implications of these findings ...
80 3gwc - An In Silico Approach for Identification of Potential Anti-Mycobacterial Targets of Vasicine and Related Chemical Compounds 2016 A Kashyap Chaliha, D Gogoi, P Chetia - chemistry & high , 2016 - ingentaconnect.com ... (Table 5). Chemical similarity search of vasicine using PubChem Structure Search yielded ... SlNo. PDB ID Protein Name Protein Name (Short) Gene Name Resolution (A ... 9 3FV5 E. coliTopoisomerase IV Topo IV b3030 1.80 10 3GWC Thymidylate synthase X ThyX Rv2754c 1.90 ...
81 3u0g - An in silico strategy for identification of novel drug targets against Plasmodium falciparum 2017 S Rout, NP Patra, RK Mahapatra - Parasitology Research, 2017 - Springer ... structure of our target protein was constructed taking multiple templates into account, namely, 1WRV (chain B), 3U0G (chain A), 1IYE (chain A), and 5E25 (chain A). The structural similarity between first template ( PDB ID 1WRV) and the modeled structure is 0.548 ...
82 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 ...
83 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
84 2khp - An NMR-guided screening method for selective fragment docking and synthesis of a warhead inhibitor 2016 RB Khattri, DL Morris, CM Davis, SM Bilinovich - Molecules, 2016 - mdpi.com ... The active site architecture of BrmGRX matches with the proposed GRX consensus active sitestructure which suggests the N ... Structures of target proteins were obtained from the Protein DataBank (PDB) [63]. The PBD code for BrmGRX is 2KHP and hGRX1 is 1JHB [19,64]. ...
85 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
86 3rmi - A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment 2016 B Ekim - academia.edu ... Four uncharacterized proteins (1IVZ, 3B4Q, 3DDE, and 4RGI) and their closest structural neighbors (2E7V, 3RMI, 3HLX, and 5BV3, respectively), printed as output by Esperite (Cosine distance between any one of the pairs were 0.0), and to be investigated further through protein nuclear magnetic resonance spectroscopy. ...
87 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% ...
88 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
89 3ecd 3h7f A novel serine hydroxymethyltransferase from Arthrobacter nicotianae: characterization and improving catalytic efficiency by rational design 2014 W Jiang, L Chen, S Yuan, B Li, Z Liu - BMC biotechnology, 2014 - biomedcentral.com ... directed mutagenesis was indicated on the three-dimensional structure of AnSHMT, which wasconstructed from the known x-ray structure of Burkholderia Pseudomallei MycobacteriumTuberculosis T.Th.Hb8 (PDB entry 3H7F, 2DKJ and 3ECD) using Swiss ...
90 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
91 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
92 3swt - Antibiotics Targeting Tuberculosis: Biosynthesis of A-102395 and Discovery of Novel Actinomycins 2015 W Cai - 2015 - uknowledge.uky.edu ... Interestingly, Cpr19 was a monomer instead of a dimer as TauD (fig 2.3.11C,PDB ID:3SWT(110)), its closest homology, suggesting that this enzyme has a distinct three dimension structure compared with other αKG:taurine dioxygenase ...
93 3k2h 3nrr, 3kgb Antifolate agents: a patent review (2006-2010) 2011 DL Wright, AC Anderson - Expert opinion on therapeutic patents, 2011 - informahealthcare.com ... Also reported for the first time in 2010 by the Seattle Structural Genomics Center for Infectious Disease is the structure of DHFR-TS from Babesia bovis bound to NADP, dUMP and pemetrexed (PDB ID: 3K2H) or raltitrexed (PDB ID: 3NRR). ...
94 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)
95 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
96 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
97 3s99 4f3p, 4gl8 An updated structural classification of substratebinding proteins 2016 GH Scheepers, JAL a Nijeholt, B Poolman- FEBS letters, 2016 - Wiley Online Library 3ejw 3s99 4rxl 1laf 2pfy Also, these SBPs do not seem to interact with TRAP, but with the related TT transporters. Although our analysis did not classify Bug27 ( PDB : 2QPQ) in E-II, visual inspection of the structure suggests it also belongs to this subcluster [37]. Cluster F
98 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
99 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
100 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
101 3rqi - A Predicted Structure for the PixD-PixE Complex Determined by Homology Modeling, Docking Simulations, and a Mutagenesis Study 2013 S Ren, R Sato, K Hasegawa, H Ohta, S Masuda - Biochemistry, 2013 - ACS Publications ... PixE Homology Modeling The amino acid sequence of PixE was obtained from the DNA DataBank of Japan (entry ... were bacterial response regulators (best 20 defined as those with the smallest E values; PDB entries 3LUF, 3N0R, 3GT7, 1QKK, 3KHT, 3RQI, 2ZQT, 2QZJ ...
102 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
103 3kjr - Are homology models sufficiently good for free-energy simulations? 2012 S Genheden - Journal of chemical information and modeling, 2012 - ACS Publications ... factor IXa (pdb code: 1rfn(36)) with 44% sequence identity and protein C (pdb code: 1aut ... Suitable template proteins for dhfr were found by a FASTA search(38) of the protein databank. ... The results of the FASTA search are summarized in Table 1. Finally, 2bl9, 3kjr, and 2oip were ...
104 3uf8 3vaw A Research on the Use of Voxel Tessellations in the Representation, Investigation and Identification of Protein Surface Atoms and Binding Sites 2012 LL Wei - 2012 - intelligentmodelling.org.uk ... 110 5-13 Visualisations for identified dock site of protein 3UF8 from both RCSB PDB and thevoxel-based method, ... The increasing number of entries being deposited into the Protein DataBank (PDB) ... al, 2007) gives a comprehensive ordering of all proteins of known structure ...
105 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
106 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
107 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.
108 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).
109 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
110 3eiy - Asn112 in< i> Plasmodium falciparum</i> glutathione S-transferase is essential for induced reversible tetramerization by phosphate or pyrophosphate 2014 I Quesada-Soriano, C Barn, R Tllez-Sanz - et Biophysica Acta (BBA , 2014 - Elsevier ... the alignment between one of the docking poses for the binding of pyrophosphate to the PfGST tetramer near the Asn112–Lys117 closed-square pattern and three of the pyrophosphatase structures (3Q4W from Thermococcus thioreducens, 3EIY from Burkholderia pseudomallei and 2AUU/1I6T from E. coli), is suspiciously good. ...
111 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
112 3krs - Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins 2012 PG Vasudev, M Banerjee? - Proteins: Structure, Function, and Bioinformatics, 2012 - Wiley Online Library ... acts as the hydrogen bond acceptor. In the available data set of 24 TIM crystal structures, there are three examples with Asn at 119, all of which (PDB IDs:1O5X, 3KRS, 1AW1) exhibit similar motifs. Interestingly, three examples with Gln at position 119 illustrated in ...
113 2kwl 2lol, 2lky Aspectos estructurales y dinmicos en la relajacin de sistemas complejos, con nfasis en agua lquida, sobreenfriada y nanoconfinada 2015 SR Accordino - 2015 - repositoriodigital.uns.edu.ar prctico: previene la agregacin de dos placas de grafeno. Page 9. 9 Abstract In this Thesis we studied, by means of molecular dynamic simulations, the structural and We also determined the geometrical quality of the local structure of these kinds of molecules. In
114 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
115 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
116 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
117 3f0d 4l83, 4lsm, 4lhr, 3swo, 4nbr, 4kzp, 4mpq, 4kyx, 3urr, 3v7n, 4lsb, 4ni5, 3pme, 4maq, 3quv, 4lfy, 3qxz, 4efi, 3uw3, 4nim, 3m1x, 4mg4, 4lc3, 4jqp, 3laa, 4kzk, 4ijn, 4lvu, 3te8, 3md7, 3mqd A Study of Residue Contact Number Among the Amino Acid and Structural Alphabet 2015 - 2015 - chur.chu.edu.tw ... present in the protein inside or outside with the local secondary structure and demonstratePage 4. iii ... Keyword: Structural Alphabet, Amino Acid Interaction, Amino Acid contact, scoringmatrix Page 5. ... 3-1PDB DSSP .... ...
118 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
119 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
120 4pq9 - A sweet new wave: structures and mechanisms of enzymes that digest polysaccharides from marine algae 2014 JH Hehemann, AB Boraston, M Czjzek - Current opinion in structural , 2014 - Elsevier ... CAZy family, Protein, PDB codes. GH16, -Carrageenase (Pseudoaltermonas carragenovora), 1DYP. -Agarase ... -Porphyranase B (Zobellia galactanivorans), 3JUU. -1,3-Glucanase (Mycobacterium marinum M), 4PQ9. Laminarinase (Thermotoga ...
121 3meq - Asymmetric reduction of diketones by two Gluconobacter oxydans oxidoreductases 2012 P Schweiger, H Gross, J Zeiser? - Applied Microbiology and Biotechnology, 2012 - Springer ... identity, >70 % similarity) to other alcohol dehydrogenase with known 3-D structure, for example, to zinc-dependent alcohol dehydrogenases from Brucella suis (PDB, 3MEQ_A), Pseudomonas ... 2004), 3MEQ from B. suis, and 1RJW from G. stearthermophilus (Ceccarelli et al. ...
122 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.
123 4h3e - A theoretical study on the reaction pathways of peroxynitrite formation and decay at nonheme iron centers 2014 AA Attia, R Silaghi-Dumitrescu - International Journal of Quantum Chemistry, 2014 - Wiley Online Library ... The quantum chemical calculations were performed on four chemical models. These models comprised the active sites of SOR from Pyrococcus furiosus (PDB id 1DQI) and FeSOD from Trypanosoma cruzi (PDB id 4H3E) in their ferrous and ferric forms. ...
124 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
125 3ido 3jvi Atomic resolution crystal structure of< i> Vc</i> LMWPTP-1 from< i> Vibrio cholerae</i> O395: insights into a novel mode of dimerization in the Low molecular Weight 2014 S Nath, R Banerjee, U Sen - Biochemical and Biophysical Research , 2014 - Elsevier ... Several structures of LMWPTP from eukaryotic organism such as human- HCPTPA (PDB: 5PNT) [4], bovine BPTPA (PDB: 1Z12) [5], mouse RPTPA (PDB: 2P4U) [6], yeast LTP1 (PDB: 1D1P) [7] and protozoan parasite Entameoba histolytica EhPtp (PDB: 3IDO) [8] are ...
126 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).
127 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
128 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%).
129 3rqi - A variable active site residue influences the kinetics of response regulator phosphorylation and dephosphorylation 2016 RM Immormino, RE Silversmith, RB Bourret - Biochemistry, 2016 - ACS Publications ... reaction kinetics by altering access to the active site while not perturbing overall protein structure . ... Collectively, our biochemical and structural analyses indicate that position T+1 affects access to the ... (A) Surface representation of the E. coli CheY active site ( PDB entry 1fqw). ...
130 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.
131 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
132 3ndn - Bacterial methionine biosynthesis 2014 MP Ferla, WM Patrick - Microbiology, 2014 - Soc General Microbiol ... 2). Its presence in P. aeruginosa and P. putida has been discussed (Foglino et al., 1995; Alaminos & Ramos, 2001), and an unpublished structure of a Mycobacterium tuberculosis O-succinylhomoserine thiolase has been deposited in the Protein Data Bank (PDB ID 3NDN). ...
133 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
134 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.
135 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
136 3tl6 - Basic Exploratory Proteins Analysis with Statistical Methods Applied on Structural Features 2015 E Del Prete, S Dotolo, A Marabotti- Mathematical Models in, 2015 - Springer 1JP7, 1M73, 1ODK, 1PK9, 1QE5, 1TCU, 1V4N, 1VMK, 1XE3, 1Z33, 2P4S, 3KHS, 3OZE, 3SCZ, 3TL6 , 3UAV, 4D98 2. Different online and local tools have been used to extract protein structural properties from PDB files: Vadar [15], for secondary structure (also confirmed
137 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
138 3grp 3f9i BdcA, a Protein Important for Escherichia coli Biofilm Dispersal, Is a Short-Chain Dehydrogenase/Reductase that Binds Specifically to NADPH 2014 DM Lord, AU Baran, TK Wood, W Peti, R Page - PloS one, 2014 - dx.plos.org ... Table 2. BdcA structural homologs as determined by DALI and FFAS. ... Indeed, the same loopsare disordered in the protein whose structure is most similar to BdcA, Bartonella henselae FabG(PDB 3GRP; Table 2) and Rickettsia prowazekii FabG (PDB 3F9I; Table 2) [14]. ...
139 4ggq - BECN2 interacts with ATG14 through a metastable coiledcoil to mediate autophagy 2017 M Su, Y Li, S Wyborny, D Neau, S Chakravarthy - Protein , 2017 - Wiley Online Library ... CCDs are unique in terms of protein folding because their tertiary structures, and often theirsecondary structure as well, are coupled to their oligomerization.34 Therefore, we assessed andcompared structural stability of the WT and seven mutant BECN2 CCD constructs using ...The atomic structures of MBP (extracted from PDB code 4GGQ), SUMO (extracted from PDB code 1L2N) and the BECN2:ATG14 CCD model were used in SASREF to build a model that was fit into the corresponding SAXS ...
140 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...
141 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
142 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
143 4n5f 4m9a Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for ProteinProtein Interactions 2017 BS Kang, GK Pugalendhi, KJ Kim- Molecules, 2017 - mdpi.com ... To determine the interactions between protein structures , they used the solvent-excluded surface (SES) for each protein structure , measured the distance between point pairs from two solvent-excluded ... PISA is used to select the dimeric structure in the PDB (Protein Data Bank ... Table 1. Computed binding directions and area ratios. 4N5F 0.681050
144 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 ...
145 3q8n - Biocatalytic Synthesis of Amino Alcohols 2015 H Kohls - 2015 - d-nb.info ATA Amine transaminase PDB Protein data bank Nevertheless, the structural scope of amines accessible with high yields and high optical pu- rities by these methods is Ver- nakalant, a 1,2-amino alcohol used as antiarrhythmic drug (see Figure 1 for the structure of Vernakalant
146 4o2d - Biochemical and Structural Characterization of Mycobacterial Aspartyl-tRNA Synthetase AspS, a Promising TB Drug Target 2014 SS Gurcha, V Usha, JAG Cox, K Fütterer, KA Abrahams… - PloS one, 2014 - dx.plos.org ... The corresponding loop in E. coli AspRS is 11 amino acid residues shorter (Figure 7). Anapo-structure of Ms-AspS has recently been deposited in the PDB (entry 4O2D), in which thisloop assumes a very different conformation, forming a 2-turn α-helix and folding back ...
147 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
148 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
149 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).
150 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
151 4lsm - Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica 2014 VL Zinsser, EM Hoey, A Trudgett, DJ Timson - Biochimica et Biophysica …, 2014 - Elsevier ... other parasites, for example Plasmodium falciparum (PDB: 1YWG [52]; rmsd 1.226 Å over 8358equivalent atoms) Trypanosoma brucei (PDB: 2X0N, [53]; rmsd 2.009 Å over 8522 equivalentatoms) and Trypanosoma cruzi (PDB: 4LSM, note that this structure only contains ...
152 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
153 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
154 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
155 4q12 4pzu Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis 2017 MM Dunsirn, JB Thoden, M Gilbert, HM Holden - Biochemistry, 2017 - ACS Publications ... and 4Q12). Whereas this protein was suggested to be a sugar N-formyltransferase, ... RelevantX-ray data collection statistics are listed in Table 1. The structure was solved via molecularreplacement with PHASER21 and using PDB entry 4PZU as a search probe. ...
156 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
157 3nfw - Biochemical properties and crystal structure of the flavin reductase FerA from Paracoccus denitrificans 2016 V Sedlek, T Klumpler, J Marek, I Kuera - Microbiological Research, 2016 - Elsevier ...Sequence and structural comparisons of FerA with a flavin reductase like domain protein family (PF01613). 3NFW E5Q9D7 NmoB Mycobacterium thermoresistibile ...
158 3rr2 - Biochemical properties of nematode< i> O</i>-acetylserine (thiol) lyase paralogs imply their distinct roles in hydrogen sulfide homeostasis 2013 R Vozdek, A Hn?zda, J Krijt, L ?er?, V Ko?ich - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2013 - Elsevier ... First, their amino acid sequences, together with sequences of OAS-TL (PDB ID: 1D6S, 1FCJ, 1O58, 1VE1, 1Y7L, 1Z7W, 2EGU, 2JC3, 2PQM, 2Q3D, 2V03 and 3RR2) and CBS (PDB ID: 1JBQ and 3PC3) were aligned using MUSCLE 3.8.31 [23]. ...
159 3oec - Biochemical Studies and Ligand-bound Structures of Biphenyl Dehydrogenase from Pandoraea pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme 2011 S Dhindwal, DN Patil, M Mohammadi? - Journal of Biological Chemistry, 2011 - ASBMB ... PDB code 1BDB and BphB B-356 are shown in black color, and other structures are shown in light colors. These PDB codes are: 2HQ1, 3OEC, 3PKO, 2UVD, 2PNF, 2WSB, 1YDE, 2WDZ, 1HDC, and 1NFR. Reactivity of BphB B-356 with Polychlorinated Biphenyls. ...
160 3q8n - Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications 2015 F Steffen-Munsberg, C Vickers, H Kohls, H Land… - Biotechnology …, 2015 - Elsevier In this review we analyse structure/sequence-function relationships for the superfamily ofPLP-dependent enzymes with special emphasis on class III transaminase.
161 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
162 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
163 3glq - Biological activity on cordycepin and cordycepin triphosphate based on the reverse molecular docking 2016 Gong, Guocai , Ling et al. - (J. Hunan Agr. Un. (Nat Sci) ), 2016 - xb.cnjournals.com 12.83 3IID 8.89 2XZL 12.35 1ZOS 8.85 3LBN 12.34 3GLQ 8.75 1F2U 1QQO PDB 1 ADP Fig.1 Comparison the structure conformation
164 4hjh 3uw2 Biology, Mechanism, and Structure of Enzymes in the -d-Phosphohexomutase Superfamily 2017 KM Stiers, AG Muenks, LJ Beamer - in Protein Chemistry and Structural , 2017 - Elsevier ... Enzymes in the α-d-phosphohexomutases superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life and are required for a myriad of cellular processes, ...
165 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
166 3rd5 - Biomedical Informatics and Computational Biology for High-Throughput Data Analysis 2014 J Wang - downloads.hindawi.com ... Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure ofProteins, Shambhu Malleshappa Gowder, Jhinuk Chatterjee, Tanusree Chaudhuri,and Kusum Paul Volume 2014, Article ID 971258, 7 pages ...
167 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
168 3s4k - Biosynthesis and Cellular Actions of Bioactive Natural Products 2015 S Mori - 2015 - oaktrust.library.tamu.edu The structure of AziG was determined using the molecular replacement method, with Mycobacterium tuberculosis thioesterase (PDB ID: 3S4K) as the model.
169 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
170 3svk - Bsqueda racional de blancos teraputicos para atacar al bacilo de la tuberculosis en la fase de latencia 2014 BIM Kruk, Q Biolgica, UBA de Buenos Aires - repositoriouba.sisbi.uba.ar ... certain Protein Family (PFAM) sequence homology, for which exists at least one molecularstructure listed in the Protein Data Bank (PDB). Subsequently metabolic and essentialityinformation was considered to classify the lead compounds obtained. Rv0859 3SVK (0.850) fadA Putative acyltransferase...
171 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
172 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
173 4ed9 - C7orf10 encodes succinate-hydroxymethylglutarate CoA-transferase, the enzyme that converts glutarate to glutaryl-CoA 2014 S Marlaire, E Van Schaftingen… - Journal of inherited …, 2014 - Springer ... Electrophoresis was performed with ≈50 μg protein for the Coomassie Blue stained gel and ≈5 μg (soluble proteins) or ≈1 ... The closest homologue of human C7orf10 for which a structure is available (4ED9) shares more than 40 % se- quence identity with the mammalian ...
174 3nfw - Camphor Pathway Redux: Functional Recombinant Expression of 2, 5-and 3, 6-Diketocamphane Monooxygenases of Pseudomonas putida ATCC 17453 with Their Cognate Flavin Reductase Catalyzing Baeyer-Villiger Reactions 2013 H Iwaki, S Grosse, H Bergeron, H Leisch? - Applied and Environmental Microbiology, 2013 - Am Soc Microbiol ... The closest homolog whose structure has been determined is nitrilotriacetate monooxygenase component B (NTA-MoB) (189 amino acids) derived from Mycobacterium thermoresistibile that was characterized as a homodimer with a split-barrel motif typical of short-chain flavin reductases (PDB ID 3NFW) ...
175 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
176 2lwk - Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA-Ligand Poses? 2016 AT Frank - Journal of Chemical Information and Modeling, 2016 - ACS Publications ... shift data within standard procedures to aid in efficiently determining the 3D structure ofRNA-ligand complexes by acting as an additional source of structural information that is 4 Page4 of 30 ... promoter-DPQ complex (PDBID: 2LWK, BMRBID: 18633)37 (see Fig. 1). ...
177 3p96 3km3, 3k9g Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal 2016 TC Terwilliger, G Bunkczi, LW Hung - Section D: Structural , 2016 - scripts.iucr.org ... Journal logo, STRUCTURAL BIOLOGY. ... 49-93.] ) that accounts for over 70% of depositions of experimentally phased structures in the Protein Data Bank (PDB; Berman et ... requires a specific element to be present at a limited number of sites in the macromolecular structure and the ...
178 3khw - Caracterização dos genes codificadores da hemaglutinina e PB2 do vírus Influenza A (H1N1) pandêmico isolado na mesorregião metropolitana de Belém 2012 JA FERREIRA - 2012 - repositorio.ufpa.br ... LACEN Laboratório Central MDCK Cultura de células de rim canino (Madin Darbin Canine Kidney)Mrna Ácido ribonucléico mensageiro M631L Substituição no aminoácido 631 de uma metioninapor uma leucina OMS Organização Mundial da Saúde PDB Banco de dados de ...
179 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
180 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
181 4ix8 - Caracterizacin estructural y funcional de la tirosina aminotransferasa de leishmania infantum 2016 M Moreno Izquierdo - 2016 - repositorio.uam.es ... Consequently the PLP-bonded structure of this enzyme was solved by X-raycrystallography at 2.35 of resolution. A comprehensive basis for the mechanismof the transamination in the active center allowed a structure-based ...
182 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
183 4f4h - Caracterizao de enzima nad sintetase (NADE2) de herbaspirillum seropedicae 2016 ARS Santos - 2016 - acervodigital.ufpr.br ... Outras NAD sintetases de procariotos com domínio glutaminase como a de Cytophaga hutchinsonii (número PDB 3ILV) e Burkholderia thailandensis (número PDB 4F4H), possuem estruturas cristalinas determinadas e depositadas no banco de dados PDB. ...
184 3i3r 3nrr Caracterizao estrutural e avaliao da atividade biolgica de uma nova hipotensina identificada no veneno do escorpio Tityus stigmurus 2016 RJA Machado - 2016 - repositorio.ufrn.br ... This study aimed to carry out the structural characterization and biological evaluation of a new hypotensin identified in T. stigmurus scorpion venom. The cluster TSTI0006C, obtained from the venom gland transcriptome, was analyzed and had its primary structure reduced after ...
185 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
186 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).
187 3gaf - Carboxyl-Terminal and Arg38 are Essential for Activity of the 7α-Hydroxysteroid Dehydrogenase from Clostridium absonum 2014 D Lou, B Wang, J Tan, L Zhu - Protein and peptide letters, 2014 - ingentaconnect.com ... E. coli (Ec 7α-HSDH, PDB code: 1FMC) [21] and Brucella melitensis (PDB code: 3GAF) havebeen ... and arginine at position 37 of the human estro- genic 17β-HSDH (PDB code: 1QYV ... 38 isof vital importance, and the residue- replacement disrupts the normal structure for cofactor ...
188 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)
189 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
190 3fvb - Catalysis of iron core formation in Escherichia coli bacterioferritin 2009 S Wong - 2009 - circle.ubc.ca ... Another example of a small molecule occupying a ferroxidase pore was recently discovered through crystallographic analysis of BFR from Brucella melitensis (PDB ID: 3FVB). This structure revealed imidazole bound to iron at the ferroxidase site such that the imidazole is located in the ferroxidase pore directly between the ferroxidase site and the pore opening. ...
191 3obk - Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations 2012 B Tian, E Erdtman, LA Eriksson - The Journal of Physical Chemistry, 2012 - ACS Publications ... 2. Computational Details The crystal structures of the yeast PBGS-PBG* intermediate (PDB code 1OHL 7 ) and the Toxoplasma gondii PBGS-PBG complex (PDB code 3OBK 10 ) were obtained from the RCSB Protein Data Bank. Monomers of the two structures were used. ...
192 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
193 3py6 - Cation-PI Interactions in beta-Lactamases: The Role in Structural Stability 2012 P Lavanya, S Ramaiah, A Anbarasu - Cell biochemistry and biophysics, 2012 - Springer ... 3PY6-A K37?Y263 -5.33 -1.41 -6.74 K231?W228 -8.02 -1.66 -9.68 2G2W-A R266?F66 -1.62 -1.06 -2.71 R259?W290 -7.01 -4.74 -11.75 K34?W60 -2.81 -0.75 -3.56 Cell Biochem Biophys 123 Page 3. Table 1 continued PDB ID Cation?p interacting residues ...
194 4fry - CBS domains: Ligand binding sites and conformational variability 2013 J Ere?o-Orbea, I Oyenarte, LA Mart?nez-Cruz - Archives of biochemistry and biophysics, 2013 - Elsevier ... At present 120 crystal structures containing 52 different ligands have been reported in the protein data bank (PDB). Of these, 56 entries correspond to eukaryal, 47 to bacterial and 17 to archaeal proteins, respectively. Among ...
195 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
196 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
197 3pm6 - Chapter 2. Aldolase oligomerization relates to specific dynamics essential to carry out its function 2013 AR Katebi, RL Jernigan, LHB Center - Building and simulating protein machines, 2013 - lib.dr.iastate.edu ... used in the multiple sequence alignment, we use subunits from the following PDB Ids: B. anthracis?3Q94; C. immitis?3PM6; C. jejune ... software suite [13-15] to model the missing loop regions of the FBA structures retrieved from the Protein Data Bank [16 ... E. coli FBA: PDB Id?1ZEN ...
198 3gvg 3krs Chapter 3. Triosephosphate Isomerase Structure Space Diversity: oligomerization, dynamics, and functionality - an evolutionary perspective. 2013 AR Katebi, RL Jernigan - Building and simulating protein machines, 2013 - lib.dr.iastate.edu ... TIM Structure Database: We have downloaded 121 TIM structures from the Protein Data Bank (PDB)(www. ... 105 PDB ids of the TIM structures that are used to extract these 263 chains ... 2VFF 2VFG 2VFH 2VFI 2VOM 2VXN 2WSQ 2X1R 2X1S 2X1T 2X1U 2YPI 3GVG 3KRS 3M9Y ...
199 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
200 3hn6 - Characterisation of NagA and NagB from methicillin-resistant Staphylococcus aureus. 2017 JS Davies - 2017 - ir.canterbury.ac.nz Borrelia burgdorferi ( PDB : 3HN6 ). Described as a having a three-layer // sandwich fold shape information and build ab initio models depicting the 3-D structure of MRSA NagA in solution Given the divergence of active site architecture and metal
201 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
202 3ngj - Characterization and application of a newly synthesized 2-deoxyribose-5-phosphate aldolase 2013 ZY You, ZQ Liu, YG Zheng, YC Shen - Journal of industrial microbiology & Biotechnology, 2013 - Springer ... The crystal structures of DERAs from Entamoeba histolytica (PDB accession NO. 3NGJ) and Thermotoga maritima (PDB accession NO. 3R12) were used as templates. ... 3NGJ, resolution 1.70 A?) and Thermotoga maritima (54.3 % identity; PDB accession no. ...
203 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
204 4odj - Characterization and redox regulation of Plasmodium falciparum methionine adenosyltransferase 2016 J Pretzel, M Gehr, M Eisenkolb, L Wang - Journal of , 2016 - Jpn Biochemical Soc ... The structure of PfalMAT was modelled according to the crystal structures of MAT2A fromHomo sapiens (PDB no. 2p02) and Cryptosporidium hominis (PDB no. 4odj) using theSWISS-MODEL automated comparative protein-modelling server (36). ...
205 3nf4 - Characterization by solution small angle X-ray scattering of the oligomeric state of structural genomics protein targets. 2013 K Basil - 2013 - dspace.sunyconnect.suny.edu ... Then, the smallest asymmetrical unit (ASU) of the crystal is deposited in the Protein Data Bank (PDB)2. ... These proteins, called by the PDB codes 3NF4, 3LKE, 3KFO and 3NF2, were associated with an already known crystal structure listed in the PDB archive. ...
206 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 )
207 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
208 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
209 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,
210 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
211 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
212 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. ...
213 3l56 - Characterization of influenza A viruses with polymorphism in PB2 residues 701 and 702 2017 AWH Chin, NKC Leong, JM Nicholls, LLM Poon- Scientific Reports, 2017 - nature.com Correlation between the structural predictions and the polymerase activities in 293T cells at 37 C. In order to anticipate the effect of PB2-701 and 702 mutations on surface charge distributions, protein models of PB2-701 and 702 mutants ( PDB ID: 3CW4, 3L56 and 2GMO) were
214 3p96 - Characterization of M. tuberculosis SerB2, an Essential HAD-Family Phosphatase, Reveals Novel Properties 2014 GP Yadav, S Shree, R Maurya, N Rai, DK Singh… - PloS one, 2014 - dx.plos.org ... BLAST [22] search against the NCBI database with MtSerB2 revealed highest similarity (83%)with M. avium SerB whose X-ray structure has recently been reported [17]. Homology modelsof MtSerB2 based on M. avium SerB (PDB code 3P96) were generated using ...
215 3qh4 - Characterization of Mycobacterial Estrases/Lipases using combined Biochemical and Computational Enzymology 2012 A SHUKLA - 2012 - scholarbank.nus.edu ... Page 12. 3 Lists of Abbreviations THL: Tetrahydrolipstatin pNP: para-nitrophenol PDB: ProteinData Bank PMSF: phenylmethanesulfonylfluoride E600: diethyl-p-nitrophenylphosphate EC : Enzyme classifier TAGs: Triacylglycerol MTB: Mycobacterium tuberculosis ...
216 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
217 3k2h - Characterization of natural product biological imprints for computer-aided drug design applications 2015 N Sturm - 2015 - theses.fr ... Changes in sequence and structure also explain the poor similarity between SB4 inhibitor-binding sites in Mitogen-activated protein (MAP) kinase 14 and MAP kinase 1 (PDB codes: 1bl7, 3erk), and between the antifolate LYA-binding site in human and protozoan thymidylate synthases (PDB codes: 1juj, 3k2h). ...
218 3k9w 3pxu Characterization of Phosphopantetheine Adenylyltransferase: A Potential, Novel, Antibacterial Target 2013 T Wubben - 2013 - indigo.lib.uic.edu ... PDB Protein Data Bank PEG polyethylene glycol PhP 4'-phosphopantetheine Pi orthophosphate ...root mean standard deviation rpm revolutions per minute SAR structure-activity relationship ...thermodynamic, and structural characterization of M.tuberculosis and B.anthracis PPAT ...
219 3qhd 3f0d, 3jvh, 3k14, 3mbm Characterization of potential anti-infective agents of Burkholderia pseudomallei targeting IspF 2016 JM Blain - 2016 - search.proquest.com 103 Page 16. xiii Figure 3-3 Docking HGN-0006/HGN-0007 display structural differences in binding . 106 Page 22. xix PDB protein data bank PEEK polyether ether ketone rpm rotations per minute SAR structure activity relationship SDS sodium dodecylsulfate SE size exclusion
220 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
221 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 ...
222 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
223 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
224 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
225 3ndn - Characterization of the Side-Chain Hydroxyl Moieties of Residues Y56, Y111, Y238, Y338, and S339 as Determinants of Specificity in E. coli Cystathionine beta-Lyase 2011 PH Lodha, SM Aitken - Biochemistry, 2011 - ACS Publications ... figure Scheme 2. Observed Contacts of the PLP-AVG External Aldimine Active Site of eCBL a. a The dotted lines represent putative hydrogen bond distances of ?3.3 ? between heteroatoms. The image was constructed using ChemDraw and PDB entry 1CL2.(3). ...
226 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
227 4efz - Characterizations of Two Bacterial Persulfide Dioxygenases of the Metallo-β-lactamase Superfamily 2015 SA Sattler, X Wang, KM Lewis, PJ DeHan… - Journal of Biological …, 2015 - ASBMB ... The statistics for the diffraction data are listed in Table 1. Initial phasing of apo- form PpPDO2diffraction data was conducted by molecular replacement with the PDB coordinates of model4EFZ using PHENIX Phaser (18). ... RESULTS Global Structure ...
228 3v7o 3tcq Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions 2014 S Chakraborty, B Rao, B Asgeirsson… - …, 2014 - f1000research.com ... 1EBO,2EBO,3VE0,3CSY.. 2I8B,3V7O 3FKE,3L25,4LG2,4IBK... ... A PDB database search usingthe keyword 'Ebola' generate 146 single chained proteins, which were analyzed using DefineSecondary Structure of Proteins, resulting in 758 alpha helices (ALPHA.zip). ...
229 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).
230 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
231 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
232 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
233 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
234 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
235 3e7d 3uk1 CH pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability 2014 M Kumar, PV Balaji - Journal of molecular modeling, 2014 - Springer ... The coordinates of proteins included in the dataset were downloaded from the protein databank [33]. ... discoideum non-muscle type myosin-2 heavy chain (PDB id 3BZ9). ... Brucella abortus CobH, precorrin-8X methylmutase 3E7D D Phe16:CE1 Tyr12 2.83 1.84 172 66 ...
236 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)
237 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
238 4dz4 - Clonamiento y anlisis funcional de la agmatinasa de ratn 2016 R Carrera, N Natalia - 2016 - repositorio.udec.cl Page 1. Universidad de Concepcin Direccin de Postgrado Facultad de Ciencias Biolgicas - Programa de Magster en Bioqumica y Bioinformtica Clonamiento y anlisis funcional de la agmatinasa de ratn. Tesis para optar PDB ID: 4DZ4. X -ray crystal structure of a hypothetical Agmatinase from Burkholderia thailandensis. ...
239 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
240 2kwl 2l4b Cloning, expression and characterisation of the starter module from indanomycin biosynthesis 2014 SR Derrington - 2014 - etheses.whiterose.ac.uk Both structure calculations produced comparable structures for IdmK. The structure 137 4.5 Structure determination using NMR spectroscopy ..... 139 4.5.1 Initial analysis of the suitability of IdmK for structural studies by NMR ... Further validation was carried by comparison with known canonical acyl carrier protein folds (PDB codes: 1HY8, 1T8K, 1VKU, 2AVA, 2CGQ, 2GDW, 2KOO, 2KWL and 2L0Q) (X
241 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
242 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
243 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- Fruits, 2017 - search.ebscohost.com respectively. Molecular docking study was performed on 3D structure of ANR obtained from homology modeling technique to check binding interaction of template molecule ( PDB ID: 4K6F ) with bound ligand (NADP). Ligand
244 3ijp 4f3y Cloning, expression, crystallization and preliminary structural studies of dihydrodipicolinate reductase from Acinetobacter baumannii 2013 S Kaushik, A Singh, M Sinha, P Kaur? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... 143, 617-623.] ), Bartonella henselae (BhDHDPR; PDB entry 3ijp ; Seattle Structural Genomics Center for Infectious Disease, unpublished work), Burkholderia thailandensis (BtDHDPR; PDB entry 4f3y ; Seattle Structural Genomics Center for Infectious Disease, unpublished ...
245 3ld9 3v9p Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of thymidylate kinase (TTHA1607) from Thermus thermophilus HB8 2013 SK Chaudhary, J Jeyakanthan? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... aureus (PDB entry 4f4i ; Midwest Center for Structural Genomics, unpublished work), Burkholderia thailandensis (PDB entry 3v9p ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Ehrlichia chaffeensis (PDB entry 3ld9 ; Leibly et al., 2011 [Leibly ...
246 3hja - Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus 2014 R Nagarajan, K Ponnuraj - Acta Crystallographica Section F: , 2014 - scripts.iucr.org ... 246, 511-521.] ), Borrelia burgdorferi (PDB entry 3hja ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and E. coli (PDB entry 1s7c ; Berkeley Structural Genomics Center, unpublished work) and fungal species as Saccharomyces cerevisiae (PDB ...
247 3kre - Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of SAICAR synthase from Streptococcus suis serotype 2 2010 X Cheng, G Lu, J Qi, H Cheng, F Gao? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2010 - scripts.iucr.org ... F62, 335-339.] ), Ehrlichia chaffeensis (PDB code 3kre ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Pyrococcus horikoshii OT3 (Manjunath et al., 2010 [Manjunath, K., Jeyakanthan, J., Nakagawa, N., Shinkai, A., Yoshimura, M., Kuramitsu, S ...
248 3ijp - Cloning overexpression purification and characterization of DAPB gene encoding dihydrodipicolinate reductase of pseudomonas aeruginosa PAO1 2016 V Anand - 2016 - ir.inflibnet.ac.in ... preliminary crystallization reports have been published for Staphylococcus aureus (Dommarajuet al., 2010) and Bartonella henselae (PDB code 3IJP) as well. ... biosynthesis enzyme from P.aeruginosa PAOl is an essential step to finally determine its 3-D structure and can ...
249 3khp - Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of Rv0241c (HtdX) from Mycobacterium tuberculosis H37Rv 2013 R Biswas, D Dutta, AK Das - Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... PDB entry, Identity (%), Query cover (%), Reference. 1pn2, 47, 10, Koski et al. (2004 [Koski, MK, Haapalainen, AM, Hiltunen, JK & Glumoff, T. (2004). ... F66, 272-274.] ). 3khp, 36, 19, Seattle Structural Genomics Center for Infectious Disease (unpublished work). 3oml, 33, 37, Haataja ...
250 3ido - Cloning, purification, crystallization and preliminary X-ray analysis of two low-molecular-weight protein tyrosine phosphatases from Vibrio cholerae 2012 S Nath, R Banerjee, S Khamrui, U Sen - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... Biol. 215, 403-410.] ) search for a homologous structure showed that the amino-acid sequence of VcLMWPTP-1 possesses the highest identity (43%) to that of protein tyrosine phosphatase from Entamoeba histolytica (PDB entry 3ido ; Seattle Structural Genomics Center for ...
251 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
252 3d5t 3doc 'Cold spots' in protein cold adaptation: Insights from normalized atomic displacement parameters (< i> B'</i>-factors) 2010 A Siglioccolo, R Gerace, S Pascarella - Biophysical chemistry, 2010 - Elsevier ... Growth temperature of the microorganism sources of the selected proteins were taken from thedatabank DSMZ (http://www.dsmz.de/, Deutsche Sammlung von ... Family, Source a, Growth T (?C) b, Pdb ID c, Res. ... Burkholderia pseudomallei, 40, 3D5T, 2.51, 253/328 (77%), 2, 331. ...
253 3tcq - CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments 2015 CLE Zhou - Source Code for Biology and Medicine, 2015 - Springer ... there exist crystal structures for several of the filovirus VP40 proteins [ 21 ] (Sudan: 3TCQ, 4LD8;Zaire: 4LDB, 4LDD, 4LDM; Ebola sp.: 1ES6, 1H2C, 1H2D), structure models for ... models for proteinsthat are represented in the Protein Data Bank database (PDB) will naturally ...
254 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
255 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)
256 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
257 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%),
258 2kwl - Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction 2012 J Lehtivarjo, K Tuppurainen, T Hassinen? - Journal of biomolecular NMR, 2012 - Springer ... enough. Furthermore, in the static structure of the acyl carrier protein from Borrelia burgdorferi (PDB 2KWL) there are two large 13Ca shift prediction errors (E37Ca, 3.92 ppm and I61Ca, -3.08 ppm) in the loop regions. When ...
259 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
260 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
261 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 )
262 3qi6 - Comparative Genomics Analysis of Mycobacterium ulcerans for the Identification of Putative Essential Genes and Therapeutic Candidates 2012 AM Butt, I Nasrullah, S Tahir, Y Tong - PloS one, 2012 - dx.plos.org ... Experimentally and computationally solved 3D structures were detected by searching the Protein Data Bank (PDB) (http://www.rcsb.org/pdb) [33] and ModBase (http://salilab.org/modbase) [34] databases, respectively. Druggability. ...
263 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
264 3lgj 3pgz Comparative modelling and in-silico drug designing 2013 D Kumar, A Sarvate, S Singh? - IEEE Conference on Information & Communication Technologies (ICT), 2013 - ieeexplore.ieee.org ... Model No. Template PDB ID Percentage of residues in most favoured region of Ramachandran plot Z- score 1 1Z9F 91 -4.9 2 3TQY 93 -4.53 3 1SRU 90 -3.23 ... 8 3PGZ 88 -4.27 9 3ULL 92 -4.06 10 2DUD 95 -4.13 11 1SE8 94 -4.33 12 3LGJ 94 -5.34 13 5MDH 90 -1.48 ...
265 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
266 3rd5 - Comparatives study on sequence structure function relationship of human short-chain dehydrogenases/reductases 2013 TTN Nu - 2013 - csc.hcmiu.edu.vn ... Table 1 : PDB code and name of five representative 4. 3rd5 chain A, Retinol dehydrogenase 11...
267 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)
268 3ijp - Comparative Structure and Function Analyses of Native and His-Tagged forms of Dihydrodipicolinate Reductase from Methicillin-Resistant Staphylococcus aureus 2012 C Dogovski, SR Dommaraju, LC Small? - Protein Expression and Purification, 2012 - Elsevier ... of DHDPR from five bacterial species have been determined by X-ray crystallography, namely from E. coli [25] and [26] (PDB ID: 1ARZ), M. tuberculosis[27] (PDB ID: 1C3V), T. maritima (PDB ID: 1VM6), Bartonella hensalae (PDB ID: 3IJP) and more recently from S. aureus COL ...
269 3uam - Comparative study of two chitin-active and two cellulose-active AA10-type lytic polysaccharide monooxygenases 2014 Z Forsberg, ?K R?hr, S Mekasha, KK Andersson? - Biochemistry, 2014 - ACS Publications ... Structural Sequence Alignment PyMod(27) was used to make a structure-based sequence alignment(28) of five AA10-type LPMOs with known structures: EfAA10A (PDB entry 4A02), BpAA10A (PDB entry 3UAM), VcAA10B (PDB entry 2XWX), BaAA10A (PDB entry 2YOX), and ...
270 3rd5 - Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family 2014 NTN Tang, L Le - Evolutionary bioinformatics online, 2014 - ncbi.nlm.nih.gov ... structures within each group were compared with each other and the selected structure was the ...GROUPS, PDB CODE AND NAME OF REPRESENTATIVE STRUCTURES. ... 4, 3rd5 chain A, aputative uncharacterized oxidoreductase protein from Mycobacterium Paratuberculosis. ...
271 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)
272 3laa - Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria 2012 MD Hartmann, I Grin? - Proceedings of the ?, 2012 - National Acad Sciences ... was conducted with symmetry constraints; the membrane anchor was modeled by using the Hia membrane anchor domain (PDB ID code ... Comparable interaction patterns can be observed for a HIM2 in the partial Burkholderia pseudomallei TAA head structure 3LAA (17) (Fig. ...
273 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)
274 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
275 3py6 - Computational analysis of N-H...PI interactions and its impact on the structural stability of beta-lactamases 2014 P Lavanya, S Ramaiah, A Anbarasu - Computers in Biology and Medicine, 2014 - Elsevier ... Three dimensional structures of ?-lactamases were retrieved from Protein Data Bank (PDB) [26]. ... The PDB codes of selected 67 ?-lactamases in the dataset are as follows: ... A, 3IF6-A, 3L6N-A, 3LVZ-A, 3LY3-A, 3M2K-A, 3OPL-A, 3OZH-A, 3P09-A, 3PAE-A, 3PG4-A, 3PY6-A, 3QI0-A ...
276 3gaf - Computational analysis of the SAG 13 gene encoding an alcohol dehydrogenase 2010 M Adhikary, S Ganguli, HJ Chakraborty, P Basu et al. - Journal of Pharmaceutical and Biomedical Sciences - jpbms.info ... protein structure to be used as template using BLAST (Basic Local Alignment Search Tool) (1) against PDB (Protein Data Bank). The sequence with maximum identity and less e value was chosen and used as the reference structure for homology modeling. [3GAF, 1AE1 and ...
277 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])
278 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
279 3kw3 - Computational approach on drug targeted proteins in streptococcus pneumoniae Molecular modelling inhibitor design and docking studies 2016 TM Reddy - 2016 - ir.inflibnet.ac.in ... Sequence alignment of Sp-AIr model with crystal structure alanine racemase (1SFT) based onsequence ... Air, indicates it closely related with 1SFT compare with other PDB's (2SFP, ... 2DY3 Air,1 SFT 2SFP 1EPV 1XQK 3HA1 2VD9 2VD8 3HUR ----- 3COS 3KW3 1RCQ 20D0 I ...
280 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)
281 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 )
282 3rr2 - Computational Insights into the Mechanism of Inhibition of OASS-A by a Small Molecule Inhibitor 2013 A Bruno, L Amori, G Costantino - Molecular Informatics, 2013 - Wiley Online Library ... Table 1. List of OASS structures reported in PDB. PDB. Resolution. Organism. 1OAS. 2.20. Salmonella typhimurium. 1D6S. 2.30. Salmonella typhimurium. 1FCJ. ... 3IQH. 1.90. Haemophilus influenzae. 3IQI. 1.70. Haemophilus influenzae. 3RR2. 1.95. Mycobacterium marinum. 3T4P ...
283 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
284 3fdz 3ezn Computational methods & forcefields for protein design, structure prediction, & refinement with natural & modified amino acids 2015 GA Khoury - 2015 - search.proquest.com ... These were assessed by aligning the modied and unmodied structures containedinthe PDB with each other. (B) Structural similarity between the unmodied structure(U-PDB) and states of unmodied structure simulation (S1). ...
285 3eoo - Computational Methods for Detecting Ligand Accessible Pathways 2012 L Pravda - 2012 - is.muni.cz ... Regarding the development of computers and the rapid growth of data in worldwide databases such as the Protein Data Bank [1], there have been demands on partial substitution of chemical experiment by computational models. ...
286 3oc6 - Computational protein design: assessment and applications 2015 Z Li - 2015 - scholarworks.iupui.edu ... 53 xiii Page 14. Figure 3.8 Superposition of the target structures ( PDB ID 3PTE and 1B1U, cyan) ... These interactions are utilized in protein structure prediction and protein design. ... structural topology and function through evolution. Experimental techniques, such as ...
287 3h81 3njd, 3qk8, 3qka, 3q1t, 3pe8, 3p85, 3p5m, 3ome, 3oc7, 3myb, 3moy, 3he2 Computational studies of enzyme function and dynamics 2012 P Yin - 2012 - iris.lib.neu.edu ... Page 20. 19 List of Abbreviations Abbreviation Meaning CSA Catalytic Site Atlas PDB Protein Data Bank THEMATICS Theoretical Microscopic Titration Curves POOL Partial Order Optimal Likelihood ? Angstr?ms ?C Degrees Celsius ESR Electron Spin Resonance NMR ...
288 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
289 4iuj 4p9a Computer-Aided Drug Discovery and Protein-Ligand Docking 2015 H Li - 2015 - search.proquest.com ... In addition to PAC-PB1N structures, two apo crystal structures of PAC in the absence of PB1 have been reported recently [322]. The first is a 1.9Å resolution structure of H1N1 PAC (PDB ID: 4IUJ). The second is a 2.2Å resolution structure of H7N9 PAC (PDB ID: 4P9A)...
290 4eqy - Computer-Aided Structure-Based Drug Discovery: CXCL12, P. aeruginosa LpxA, and the Tiam1 PDZ Domain 2014 EW Smith - 2014 - scholarcommons.usf.edu ... there seems to be some noticeable variation at the C-terminal end of the third α-helix, involving dissimilar tilts compared to bacterial orthologs A. baumannii (PDB ID: 4E6U), L. interrogans (PDB ID: 3HSQ), C. jejuni (PDB ID: 3ROS), B. thailandensis (PDB ID: 4EQY),...
291 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
292 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
293 3qbp 3rd8, 3rrp Conformational changes upon ligand binding in the essential class II fumarase Rv1098c from< i> Mycobacterium tuberculosis</i> 2012 AE Mechaly, A Haouz, I Miras, N Barilone, P Weber? - FEBS letters, 2012 - Elsevier ... Overall, Rv1098c shows significant structural similarity to deposited structures of mycobacterial homologs (pdb entries 3RD8, 3RRP and 3QBP, all unpublished; Supplementary Table 1), as well as to other members of this superfamily, including aspartases, ?-crystallins ...
294 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
295 4g6c 4gnv Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress lactam antibiotic resistance 2017 G Vadlamani, KA Stubbs, J Dsir, Y Blriot - Protein , 2017 - Wiley Online Library ... iMosflm,[31] then scaled and averaged using SCALA (CCP4 package).[32] The BcNagZ:inhibitorcomplex structures were determined by molecular replacement using PHASER (from within thePHENIX package)[33] and a structure of BcNagZ (PDB ID: 4G6C) ...The position of the loop is also consistent with a previous structure of BcNagZ bound to the non-selective N-acetyl-β-glucosaminidase inhibitor 3-acetamido-4,5,6-trihydroxyazepane MM-124 (PDB ID: 4MSS)[9] and the product GlcNAc (PDB ID: 4GNV), indicating that ...
296 3gmt - Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations 2013 TP Schrank, JO Wrabl, VJ Hilser - Dynamics in Enzyme Catalysis: Topics in Current Chemistry, 2013 - Springer ... PDB structures 1AK2, 1E4V, 2AR7, 2RH5, 2XB4, 3GMT, 3NDP, each pairwise superimposed on 4AKE, the AK(e) structure are displayed. ... All adenylate kinase structures were retrieved from the Protein Data Bank (PDB) [71]. ...
297 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
298 3ek1 - Conservation of water molecules in protein binding interfaces 2012 Z Li, Y He, L Cao, L Wong, J Li - International Journal of Bioinformatics Research and Applications, 2012 - Inderscience ... Figure 6 Water-contacting structure of four aligned alanine residues in: a rat formyltetrahydrofolate dehydrogenase subunit interface (a, [PDB:2O2P]), and three betaine aldehyde dehydrogenase subunit interfaces (b[PDB:2WOX], c[PDB:1WNB] and d[PDB:3EK1]). ...
299 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. ...
300 3v7o - Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses 2016 M Pappalardo, M Juli, MJ Howard, JS Rossman- Scientific reports, 2016 - nature.com ... of both Ebola virus ( PDB structure 2I8B) and Reston virus ( PDB structure 3V7O ) VP30 are ... Structural data are available for both the Ebola virus and Reston virus VP35 ... These structures are highly conserved, however functional studies have demonstrated that Reston virus VP35 ...
301 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), ...
302 4n0w - Conserved water molecules in bacterial serine hydroxymethyltransferases 2015 T Milano, ML Di Salvo, S Angelaccio… - … Design and Selection, 2015 - Oxford Univ Press ... After PDB scrutiny, 11 structures were selected on the basis of better resolution, the absenceof point ... (2003) and Mustata and Briggs (2004) who analyzed the structural role of ... MD simulationswere carried out on the dimer in the apo form of the structure 4N0W corresponding to ...
303 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
304 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
305 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
306 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
307 2kok - Corynebacterium glutamicum survives arsenic stress with arsenate reductases coupled to two distinct redox mechanisms 2011 AF Villadangos, K Van Belle, K Wahni? - Molecular Microbiology, 2011 - Wiley Online Library ... fold (left) as representative for the ArsC1' subgroup of arsenate reductases (B), and R773 Ec_ArsC (PDB ID 1I9D ... R773 (Ec_ArsC), Vibrio cholerae [Vc_ArsC (VCV511445)], Streptococcus mutans strain UA159 [(Sm_ArsC (SMU_1651)] and Brucella mellitensis 2KOK (Bm_ArsC ...
308 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
309 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
310 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
311 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
312 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).
313 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
314 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
315 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
316 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
317 4ylg - Cryo-EM structure of the yeast U4/U6. U5 tri-snRNP at 3.7 resolution 2016 THD Nguyen, WP Galej, X Bai, C Oubridge - Nature, 2016 - nature.com ... 4: Secondary structure of the snRNAs in tri-snRNP. ... S. pombe ILS spliceosomal complex 19, 20(red, PDB 3JB9), was overlaid on GDPs found in other guanine-nucleotide binding proteins(grey, PDB coordinates: 1DAR, 2E1R, 2WRI, 1Z0I, 5CA8, 1XTQ, 4YLG, 1SF8, 5BXQ ...
318 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
319 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
320 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. ...
321 3nf4 3pfd Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis 2013 X Duan, L Zhang, D Zhou, K Ji, T Ma? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... different protein structures with the highest protein-sequence similarity to DszC [PDB entries 2vig ... 277, 12200-12207.] ), 3nf4 (24% identity; Seattle Structural Genomics Center for Infectious Disease ... and structure factors have been deposited in the Protein Data Bank (Bernstein et ...
322 3nfw - Crystallization and preliminary X-ray analysis of the reductase component of p-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii 2012 W Oonanant, J Sucharitakul, P Chaiyen? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... All of these structures share the same protein fold and lack the extra C-terminal domain found in C 1 . Recently, the structure of NTA monooxygenase component B from Mycobacterium thermoresistibile (PDB entry 3nfw ; Zhang et al., 2011 [Zhang, Y., Edwards, TE, Begley, DW ...
323 3lls - Crystallization and preliminary X-ray diffraction analysis of the high molecular weight ketoacyl reductase FabG4 complexed with NADH 2012 D Dutta, S Bhattacharyya, AK Das - Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... Teplyakov, A. (2010). Acta Cryst. D66, 22-25.] ), using a monomer of the apo FabG4 structure (PDB entry 3lls ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) as a search model. A promising result ...
324 3d64 - Crystallization and preliminary X-ray diffraction analysis of the S-adenosylhomocysteine hydrolase (SAHH) from Thermotoga maritima 2014 M He, Y Zheng, CH Huang, G Qian, X Xiao… - Structural Biology and …, 2014 - journals.iucr.org ... 17, 2134-2144.] ), Burkholderia pseudomallei (PDB entry 3d64 ; Seattle Structural GenomicsCenter for Infectious Disease, unpublished work), Trypanosoma ... This model was generated fromthe structure of Mycobacterium tuberculosis SAHH (PDB entry 3dhy ; 43 ...
325 4ege - Crystallization and preliminary X-ray diffraction analysis of Xaa-Pro dipeptidase from Xanthomonas campestris 2014 A Kumar, VN Are, B Ghosh, U Agrawal - Section F: Structural , 2014 - scripts.iucr.org ... Although the structures of XPD43 orthologues from the eubacteria Mycobacterium ulcerans, Bacillus anthracis and Thermotoga maritima (PDB entries 4ege , 3q6d and 2zsg ) have been deposited in the PDB by structural genomics consortia, none of these enzymes have been ...
326 3ftp - Crystallographic analysis and structure-guided engineering of NADPH-dependent Ralstonia sp. alcohol dehydrogenase toward NADH cosubstrate specificity 2013 A Lerchner, A Jarasch, W Meining? - Biotechnology and Bioengineering, 2013 - Wiley Online Library ... The coding sequence for RasADH (starting with Tyr2 according to the UniProt data bank accession number C0IR58) was amplified from the plasmid pEam-RasADH (Lavandera et al. ... 8 homologous ?-ketoacyl-acyl carrier protein reductase of Streptomyces coelicolor (PDB code: ...
327 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
328 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
329 4pq9 - Crystal structural basis for Rv0315, an immunostimulatory antigen and inactive beta-1, 3-glucanase of Mycobacterium tuberculosis 2015 W Dong, J Huang, Y Li, Y Tan, Z Shen, Y Song - Scientific , 2015 - ncbi.nlm.nih.gov ... was solved at a resolution of 1.7 by molecular replacement using the structure of-1,3-glucanase from Mycobacterium marinum (PDB code 4PQ9) as a ... Other than the differentsize of the cavity, the overall structure of Rv0315 was similar to that of ZgLamA GH16 (Fig. ...
330 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
331 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 ...
332 3uam - Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the basidiomycota fungus Phanerochaete chrysosporium 2013 M Wu, GT Beckham, AM Larsson, T Ishida? - Journal of Biological Chemistry, 2013 - ASBMB ... date, there are five LPMO structures from five different fungal GH61s available: H. jecorina GH61B (Protein Data Bank (PDB) code 2VTC ... PDB code 2XWX) (17), Enterococcus faecalis CBM33 (PDB code 4A02) (18), and Burkholderia pseudomallei CBM33 (PDB code 3UAM ...
333 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
334 4f4e - Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6 2015 A Bujacz, M Rutkiewicz-Krotewicz… - Biological …, 2015 - journals.iucr.org ... PDB references: PsyArAT, 4rkc complex with aspartate, 4rkd [Cited in] [Download citation ... Crystalstructure and enzymatic properties of a broad substrate-specificity psychrophilic ... Here, geneisolation, protein expression, purification, enzymatic properties and structural studies are ...
335 3oq8 - Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum 2016 Y Park, Y Cho, YH Lee, YW Lee, S Rhee - Journal of structural biology, 2016 - Elsevier ... The MoICL residues were selected based on the proposed structural and functional features ... In previous, unpublished work, we also observed nearly identical structural changes in Brucella melitensis ICL complexed with malonate (PDB 3OQ8). ...
336 4dgq - Crystal Structure and Functional Characterization of an Esterase (EaEST) from Exiguobacterium antarcticum 2017 CW Lee, S Kwon, SH Park, BY Kim, W Yoo, BH Ryu - PloS one, 2017 - journals.plos.org ... PDB code 3FOB), haloperoxidase (PDB code 1A8S), chloroperoxidase (PDB code 4DGQ), andesterase ... Comparison of EaEST structure with that of PfEST. Structural comparison usingsuperimposition between EaEST and PfEST (PDB code 3HI4, acetate-bound form) shows ...
337 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 ...
338 4kyx - Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2 2015 M Carter, AS Jemth, A Hagenkort, BDG Page… - Nature …, 2015 - nature.com ... The structure was solved by molecular replacement of the template structure file with PDB ID 4KYX using MolRep, and Arp/wARP was used for building the initial model, followed by iterative building cycles using the Refine program in Phenix ...
339 3dmo 3mpz Crystal structure determination and dynamic studies of< i> Mycobacterium tuberculosis</i> Cytidine deaminase in complex with products 2011 ZA S?nchez-Quitian, LFSM Timmers? - Archives of Biochemistry and Biophysics, 2011 - Elsevier ... Furthermore, in order to verify if these conformations are in agreement with CDA of different organism previously published, we analyzed other 13 CDA structures (PDB access codes: 3IJF, 3MPZ, 1MQ0, 3DMO, 1UX1, 2D30, 1UX0, 1UWZ, 1JTK, 2FR5, 1ZAB, 2FR6, and 3B8F) ...
340 3gka - Crystal Structure Determination and Mutagenesis Analysis of the Ene Reductase NCR 2012 S Reich, HW Hoeffken, B Rosche, BM Nestl? - ChemBioChem, 2012 - Wiley Online Library ... Figure 1. Crystal structure of the ene reductase NCR (PDB ID: 4A3U) dis- played in cartoon representation and showing prosthetic ... in the Supporting Infor- mation), 12-oxophytodienoate reductases 1 and 3 (OPR1 and OPR3) and N-ethylmaleimidine reductase (3GKA) from the ...
341 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
342 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
343 3pgz - Crystal Structure of a Monomeric Thiolase-Like Protein Type 1 (TLP1) from Mycobacterium smegmatis 2012 N Janardan, RK Harijan, RK Wierenga, MRN Murthy - PloS one, 2012 - dx.plos.org ... DALI search using this domain against the PDB shows structural similarities to a molybdenum binding protein (PDB id: 1H9K) [20] and a single strand DNA binding protein (PDB id: 3PGZ) (Seattle Structural Genomics Center for Infectious Disease; Unpublished). ...
344 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
345 4ege - Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases 2017 VN Are, SN Jamdar, B Ghosh, VD Goyal- Proteins: Structure,, 2017 - Wiley Online Library ... significant sequence homology with any of the known protein sequences in PDB . However, the structural superposition search using N-domain structure at Dali server ... M24 dipeptidase from Mycobacterium ulcerans ( PDB code: 4EGE ) sharing 14% sequence identity with it. ...
346 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
347 4w91 - Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU 2016 B Blauenburg, A Mielcarek, F Altegoer, CD Fage - PLoS , 2016 - journals.plos.org ... As no structure of B. subtilis SufS was available at the start of our study, we sought to fill this gap.BsSufS was thus crystallized and its structure was determined to 1.7 resolution by molecularreplacement using the B. suis homolog (PDB ID 4W91) [41] as a search ...
348 5i1f - Crystal structure of d-glycero--d-manno-heptose-1-phosphate guanylyltransferase from Yersinia pseudotuberculosis 2017 H Kim, J Park, S Kim, DH Shin- et Biophysica Acta (BBA)-Proteins and, 2017 - Elsevier A PSI-BLAST search targeting PDB showed that the sequences of eight crystal structures (4Y7U, 5I1F , 4ECM, 4AAW, 1WVC, 5L6S, 5B04, 2CU2) have strong The homologue structures are detected with the Dali server using a YpHddC structure as a template
349 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 ...
350 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
351 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]
352 3ftp 3lls, 3grp Crystal structure of FabG4 from< i> Mycobacterium tuberculosis</i> reveals the importance of C-terminal residues in ketoreductase activity 2011 D Dutta, S Bhattacharyya, S Mukherjee, B Saha? - Journal of Structural Biology, 2011 - Elsevier ... to 356 (loop II), and 395 to 417. Domain II is the catalytic domain and share highest sequence homology with Burkholderia Pseudomallei FabG (PDB: 3FTP, 42% in 248 residues overlap). The active site, deep-seated into the ...
353 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
354 3lls - Crystal structure of hexanoyl-CoA bound to beta-ketoacyl reductase FabG4 of Mycobacterium tuberculosis 2013 D Debajyoti, B Sudipta, R Amlan, B Rupam? - Biochemical Journal, 2013 - biochemj.org ... The structure of the FabG4?NADH complex was determined by molecular replacement in MOLREP [21] using a monomer of the apoFabG4 structure (PDB code 3LLS). ... MtFabG1 (MabA;PDB code 1UZM) and FabG4 (PDB codes 3LLS and 3Q6I) were chosen as the receptor. ...
355 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
356 3hwk - Crystal structure of< i> Salmonella typhimurium</i> 2-methylcitrate synthase: Insights on domain movement and substrate specificity 2011 S Chittori, HS Savithri, MRN Murthy - Journal of Structural Biology, 2011 - Elsevier ... In contrast, structural comparison of StPrpC with Mycobacterium tuberculosis GltA1 (MtGltA1; PDB: 3HWK; unpublished results) and Pyrococcus furiosus CS (PfGltA; type-I CS with shorter N-terminal) showed significant similarity in the core structure as well as in the flanking C-terminal extension...
357 4i1v 4i1u Crystal structure of Legionella pneumophila dephospho-CoA kinase reveals a non-canonical conformation of P-loop 2014 X Gong, X Chen, D Yu, N Zhang, Z Zhu, L Niu… - Journal of structural …, 2014 - Elsevier ... The first DPCK crystal structure was solved and reported from Haemophilus influenzae (HiDPCK,PDB code 1jjv ( Obmolova et al ... DPCK structures are also available in the PDB, such asBurkholderia vietnamiensis DPCK (BvDPCK, PDB codes 4i1u, 4i1v, Seattle Structural ...
358 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)
359 3v2i - Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Å resolution shows the closed structure of the substrate-binding cleft 2014 A Singh, L Gautam, M Sinha, A Bhushan, P Kaur… - FEBS open bio, 2014 - Elsevier ... 27], Francisella tularensis (FtPth) (PDB: 3NEA) [28] and Burkholderia thailandensis (BtPth) (PDB:3V2I) [29]. ... tripeptide (grey) from the neighbouring molecule from the structure of EcPth (PDB ID:2PTH ... with the stereochemistry of the substrate binding cleft in the structure of SpPth ...
360 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
361 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
362 3quv - Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase 2016 HN Im, HS Kim, DR An, JY Jang, J Kim, HJ Yoon - Journal of Structural , 2016 - Elsevier ... (ii) nucleic acid MTases [Rv2118c (PDB: 1I9G; Gupta et al., 2001), Rv2372c (PDB: 4L69; Kumar et al., 2014), Rv2966c (PDB: 3P9N; Sharma et al., 2015), and MAB_3226c (PDB: 3QUV)] ...
363 3mc4 - Crystal structure of serine acetyl transferase from< i> Brucella abortus</i> and its complex with coenzyme A 2014 S Kumar, N Kumar, N Alam, S Gourinath - Biochimica et Biophysica Acta ( , 2014 - Elsevier ... max SAT [10] have been previously published. The coordinates of a crystal structure of SAT from Brucella melitensis has also been deposited at the Protein Data Bank (PDB code: 3MC4). SATs from E. coli, B. melitensis, H. influenzae ...
364 3p96 - Crystal structure of tandem ACT domain-containing protein ACTP from Galdieria sulphuraria 2012 E Bitto, DJ Kim, CA Bingman, HJ Kim? - Proteins: Structure, Function, and Bioinformatics, 2012 - Wiley Online Library ... domains of other proteins including glycine cleavage system transcriptional regulator GcvR (PDB id: 1u8s; unpublished data), formyltetrahydrofolate deformylase (PDB id: 3nrb, 3n0v, and 3lou; unpublished data), and phosphoserine phosphatase SerB (PDB id: 3p96).16 The ...
365 4nps 4wgj Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin 2016 FV Stanger, A Harms, C Dehio, T Schirmer - PloS one, 2016 - journals.plos.org ... Depending on the conservation of crucial active site residues, the FIC fold serves as structuralscaffold for various enzymatic activities, mostly ...The lack of electron density of the flap of the E28G mutant has already been observed in several other FIC domain protein structures (e.g. Bep1 from Bartonella clarridgeiae, PBD: 4NPS or NmFicE102R from Neisseria meningitidis, PDB: 5CGL). ...
366 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
367 5vm8 - Crystal structure of the Legionella pneumophila Lpg2936 in complex with the cofactor SadenosylLmethionine reveals novel insights into the mechanism of RsmE 2017 N Pinotsis, G Waksman- Protein Science, 2017 - Wiley Online Library RsmE ( PDB ID 4e8b),[13] from H. influenzae ( PDB ID: 1nxz and 1vhy)[14] and from N. gonorrhoeae ( PDB ID 5vm8 ) Structure based sequence alignment using the most similar structures from seven different bacteria species reveals (i) a highly conserved C-terminal part of
368 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
369 4o2d - Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori 2017 C Songsiriritthigul, S Suebka, CJ Chen - Section F: Structural , 2017 - scripts.iucr.org ... 4a), similar to the positions of the Pro82 residue in the S. tokodaii ND- AspRS structure (Sato etal., 2007). ... Structural comparison of ND-AspRS1104 from H. pylori with those from M. smegmatis(PDB entry 4o2d; Baugh et al., 2015) and P. aeruginosa (PDB entry 4wj4 ...
370 4iuj - Crystal structure of the RNA-dependent RNA polymerase from influenza C virus 2015 N Hengrung, K El Omari, IS Martin, FT Vreede - Nature, 2015 - nature.com ... he published fragments of FluPolA (PDB accessions 4IUJ, 4AWH, 4CB4, 3A1G and 2VY7) were fitted by eye using Coot, which was used for all model building. ...
371 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
372 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
373 3hwi - Crystal structure of YnjE from Escherichia coli, a sulfurtransferase with three rhodanese domains 2009 P H?nzelmann, JU Dahl, J Kuper, A Urban? - Protein Science, 2009 - Wiley Online Library ... The tandem-domain rhodaneses from Thermus thermophilus (PDB entry 1uar), Mycobacterium tuberculosis (PDB entry 3hwi), Azotobacter vinelandii (Av_RhdA, PDB entry 1e0c) and Bos taurus (Rhodbov, PDB entry 1boi) with Z-scores of ?30 and rms deviations of about 2.2 ? ...
374 3grk - Crystal structures and kinetic properties of enoyl-acyl carrier protein reductase I from Candidatus Liberibacter asiaticus 2014 L Jiang, Z Gao, Y Li, S Wang, Y Dong - Protein Science, 2014 - Wiley Online Library ... henselae (BhFabI, PDB code 4EIT), E. coli (EcFabI, PDB code 2FHS or 1DFI,6,28 B. melitensis (BmFabI, PDB code 3GRK), S. aureus ... reductase glucose-ribitol dehydrogenase from Brucella melitensis (PDB code: 3GRK) is used as the search model. ...
375 4f82 - Crystal Structures and Reaction Mechanism of 1-Cys Peroxiredoxin from Vibrio vulnificus 2016 - 2016 - s-space.snu.ac.kr ... 2011) using a putative thioredoxin reductase from Burkholderia cenocepacia ( PDB code 4F82 ) as a search model. ... proteins. A. The dimeric unit of the VvPrx3 (C48D/C73S) structure at the reduced ... tuberculosis (green; PDB code 1XXU). ...
376 3qdf 4qku, 3rr6, 4maq, 4pfz, 3r6o Crystal structures of apo and liganded 4-oxalocrotonate decarboxylase uncover a structural basis for the metal-assisted decarboxylation of a vinylogous -keto acid 2016 SL Guimares, JB Coitinho, DMA Costa, SS Arajo - Biochemistry, 2016 - ACS Publications ... Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for ... Representative tertiary and quaternary structures of enzymes from (A) Mus musculus (PDB entry 1QCN(30)) and Burkholderia cenocepacia (PDB entry 4QKU); (B) Sulfolobus solfataricus (PDB entry 2Q18(32)); (C) Mycobacterium marinum (PDB entry 3QDF(39)) ...
377 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
378 3gwe - Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme 2009 KS Gajiwala, S Margosiak, J Lu, J Cortez, Y Su, Z Nie? - FEBS letters, 2009 - Elsevier ... bacterial species, two of which are Gram-positive organisms (E. faecalis and S. aureus[11]) and five Gram-negative (E. coli[10] and [12], H. influenzae, A. aeolicus (PDB ID: 2EBD), T. thermophilus (PDB ID: 1UB7) and B. pseudomallei (PDB ID: 3GWE)); M. tuberculosis[13] and ...
379 3qdf 3r6o, 3rr6 Crystal structures of Cg1458 reveal a catalytic lid domain and a common catalytic mechanism for the FAH family 2013 R Tingting, G Yanyan, M May, Z Wenjun? - Biochemical Journal, 2013 - biochemj.org ... Source/description, PDB ID, Resolution (?), Sequence identity (%), Aligned residues, Backbone RMSD (?). C. glutamicum/Cg1458, 4DBF, 1.90, ?, ?, ?. 4DBH, 2.00, ?, ?, ?. Mycobacterium marinum M/MMAR-1718, 3QDF, 2.05, 56.73, 245, 1.11. ...
380 3f0g - Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment 2014 J Kalinowska-T, PK Fyfe, A Dawson and WN Hunter - BMC Structural Biology, 2014 - biomedcentral.com ... Structural comparisons of IspF orthologues from the Protein Data Bank (PDB) were carried out using the DALI server [28]. Pairwise sequence identities range from 28 to 90%, Z scores from 18 to 31 and RMSD values from 0.3 to 2.5 ?. ...
381 3dmo - Crystal structures of MBP fusion proteins 2015 DS Waugh - Protein Science, 2015 - Wiley Online Library ... 65 Nineteen of the MBP fusion protein structures deposited in the PDB include surface ... Table 2. Surface Entropy Reduction Mutations in MBP and Their Participation in Crystal Contacts 3DMO D83A/K84A ...
382 4eff 4ix8 Crystal structures of Mycobacterium tuberculosis HspAT and ArAT reveal structural basis of their distinct substrate specificities 2016 N Nasir, A Anant, R Vyas, BK Biswal- Scientific reports, 2016 - nature.com ... site residues of I aminotransferases across species, we performed a structure and sequence ... The source of each sequence and PDB ID are: Pyrococcus horikoshii ArAT (1DJU ... 8 , Paracoccus denitrificans ArAT (2AY1) 18 , Burkholderia pseudomallei ArAT ( 4EFF ), C. glutamicum ...
383 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
384 3m4s - Crystal structures of RidA, an important enzyme for the prevention of toxic side products 2016 X Liu, J Zeng, X Chen, W Xie- Scientific reports, 2016 - nature.com 2DYY, dirty violet), and Entamoeba histolytica l-PSP ( PDB code 3M4S , gray) respectively unpublished), and a putative endoribonuclease l-PSP from Entamoeba histolytica ( PDB code3M4S, unpublished AtRidA is highly similar to other RidA family members in structure , and their
385 3d64 3n58 Crystal structures of S-adenosylhomocysteine hydrolase from the thermophilic bacterium Thermotoga maritima 2015 Y Zheng, CC Chen, TP Ko, X Xiao, Y Yang… - Journal of structural …, 2015 - Elsevier ... The Refseq or PDB numbers of these sequences are: T. maritima, AAC01562.1 ... 1B3R;Trypanosoma brucei, 3H9U; M. tuberculosis, 3DHY; B. melitensis, 3N58; B. pseudomallei, 3D64.The secondary structure elements (helices (α) and strands (β)) of tmSAHH are shown above ...
386 3nf4 - Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate 2017 T Hino, H Hamamoto, H Suzuki, H Yagi- Journal of Biological, 2017 - Elsevier 2B). This domain architecture and quaternary structure are also seen for the acyl-CoA dehydrogenase superfamily (25), and the structure of TdsC is very similar to that of DszC (2122, 23 Structure of FMN-bound TdsC FMN binding to TdsC resulted in no global structural changes
387 3nf4 - Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity 2017 T Hino, H Hamamoto, H Suzuki, H Yagi - Journal of Biological , 2017 - ASBMB ... replacement search models using MolRep (44). The polyalanine model from Mycobacterium thermoresistibile ( PDB ID: 3NF4 ) showed the highest score. After application of the ... All other structures were solved by molecular replacement of the apo-TdsC structure using ...
388 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
389 3gvg - Crystal structures of triosephosphate isomerase from methicillin resistant< i> Staphylococcus aureus</i> MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop 2012 S Mukherjee, A Roychowdhury, D Dutta, AK Das - Biochimie, 2012 - Elsevier ... Structural homologues to SaTIM in PDB were searched by the BLASTP server [46 ... sequence alignment of amino acid residues of SaTIM (3M9Y) with TIM from Bacillus stearothermophilus (2BTM), Thermotoga maritima (1B9B), Mycobacterium tuberculosis (3GVG), Vibrio marinus ...
390 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
391 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)
392 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 ...
393 3qh4 3s4k Cytosolic lipid inclusions formed during infection by viral and bacterial pathogens 2012 M Stehr, AA Elamin, M Singh - Microbes and Infection, 2012 - Elsevier ... Furthermore the three-dimensional structures of the esterases Rv0045c (PDB 3P2M) [48], Rv1847 (PDB 3S4K), and LipW (3QH4) from M. tuberculosis have been determined, but unfortunately it is not known whether these enzymes are involved in TAG hydrolysis. 5.5. ...
394 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
395 3sbx 3qh8 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 ... The super-types are S1) 3CYI, 3HYO, 2ZKJ, 3QUR, 3SBX , 3PNL and 2QV7; S2) 3T7M, 3L31, 3EVD, 3QXH, 3H5N and 2B56; ... classification of this type groups the set of known NTP binding sites in PDB , which are more ... PROTEINS: Structure , Function, and Bioinformatics ...
396 3sth - Deciphering the mechanism and function of stage-specific protein association with the membrane cytoskeleton of Toxoplasma gondii 2017 R Dubey - 2017 - search.proquest.com Crystal structure data of TgGAPDH1 Crystal structure data collection and refinement statistics of Toxoplasma GAPDH1, PDB code 3STH Crystallographic structures of the seven selected GAPDH proteins are solved and deposited in PDB . 62 Structure of TgGAPDH1 protein
397 2kok - Desenvolvimento de ProClaT, uma ferramenta computacional para a classificao de protenas: o caso DraB de Azospirillum brasiliense 2010 ET Rubel - 2010 - acervodigital.ufpr.br ... ORF Open Reading Frame PDB Protein Data Bank ProClaT Protein Classifier Tool RNA cidoribonucleico ... A MOLECULA FOI CRIADA COM A FERRAMENTA JMOL, UTILIZANDO O ARQUIVOPDB RETIRADO DO RCSB PDB (IDENTIFICAO DA ESTRUTURA: 4WZB). ...
398 3qhd 3q8h, 3k14 Design and synthesis of IspD, IspE and IspF enzyme inhibitors of the methylerythritol phosphate pathway 2016 GM Goshu - 2016 - search.proquest.com a fragment hit co-crystallized with Burkholderia pseudomallei (Bp) IspF ( PDB code: 3QHD ).2 Meroterpenoids contain non-isoprenoid structure Thiamine diphosphate (TDP) and Mg2+ bound to active site of E. coli DXS ( PDB code: 2O1S).68 Color: (magnesium) magenta
399 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
400 3v7o 4g50 Design of an expression system to enhance MBP-mediated crystallization 2017 T Jin, W Chuenchor, J Jiang, J Cheng, Y Li - Scientific , 2017 - ncbi.nlm.nih.gov ... 25 , GST 26 , TRX 27 , green fluorescent protein (GFP) 28 ,29 , SUMO (pdb: 3V7O and 4G50 ...platform is increasingly appreciated 38 ,39 , the optimal sequence, length, and structure of the ...The death domain superfamily is a structural motif found in many proteins that are involved ...
401 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
402 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
403 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
404 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).
405 3eoo - Design, Synthesis and Evaluation of Pyrazolo-Pyrazole Derivatives onMethylisocitratelyase Of Pseudomonas aeruginosa: Insilico and invitro study 2016 M Pulaganti, C Suresh Kumar - Journal of Biomolecular Structure , 2016 - Taylor & Francis ... possessing the highest sequence identity. We finally picked the A-chain of 1MUM and 3EOOas ... carefully editing PIR file and PDB file template.The developed .ali, .py, pdb template files ...structure of MICL with build command of modeller, using default parameters. ...
406 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
407 4lgv - Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies 2016 M Fuentealba, R Muoz, P Maturana, A Krapp - PloS one, 2016 - journals.plos.org ... Four additional G6PDH sequences were included: those from Mycobacterium avium(Actinobacteria), whose structure is known (PDB ID 4LGV), from Borreliaburgdorferi (Spirochaetes),Synechocisits (Cyanobacteria) and Chlamydophila pneumoniae (Chlamydiae). ...
408 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...
409 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
410 3h81 3qk8, 3qyr, 3r9t, 3r9s, 3qre, 3r9q, 3r6h, 3qmj, 3qxz, 3r0o, 3qka, 3qxi, 3swx, 3oc7, 3myb, 4g7f, 4je1, 3moy, 3p5m, 4di1, 3pe8, 3trr, 3tlf, 3rsi, 3rrv, 3njb, 3ome, 3p85, 3n5o, 3q1t, 4hdt, 3t3w, 3he2, 4f82, 3lg6 Development and optimization of a clustering process that utilizes active site features to identify functionally relevant groups within protein superfamilies 2015 JB Leuthaeuser - 2015 - search.proquest.com ... Key residues are identified from structural overlays ... Two protein structures of interest (3H8A blueand 2AKM purple) are aligned to a protein structure (1OEP gray ... In addition to forming ASPs, DASPcan also search the PDB and GenBank (NCBI protein) databases for proteins with ...
411 3q8h - Development of Inhibitors of the 2 C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents 2014 T Masini, AKH Hirsch - Journal of medicinal chemistry, 2014 - ACS Publications ... ofhe cocrystal structure of 81 with B. pseudomallei IspF (PDB code 3Q8H, Figure 4) shows that there is no direct interaction of 81 with the catalytic Zn2+ cation, but the presence of the bicyclic aromatic ring, engaged in hydrophobic interactions, probably compensates for this lack, resulting in a strong affinity of 81 or B. pseudomallei IspF. ...
412 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
413 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
414 4g50 4ggq Development, synthesis and structureactivity-relationships of inhibitors of the macrophage infectivity potentiator (Mip) proteins of Legionella pneumophila and 2016 F Seufert, M Kuhn, M Hein, M Weiwad, M Vivoli - Bioorganic & Medicinal , 2016 - Elsevier ... Structural comparison between BpMip and LpMip showed a high homology in the PPIase domain. ...A (left) and region B (right) of lead compound CJ168 (shown in orange in PDB structure 4G503 ). The ... In fact, from the BpMip crystal structures and the LpMip docking modes, the ...
415 3uk1 3upt Développement de biocapteurs ampérométriques pour la détermination de l'activité de la transcétolase et pour la détection d'inhibiteurs de cette enzyme 2013 N Touisni - 2013 - tel.archives-ouvertes.fr ... I.1.1.2. Structures tridimensionnelles des transcétolases ..... 11 ... biomolécules dans unematrice hôte apparait comme une méthode assez efficace tout en veillant à maintenirla structure de la biomolécule et son accessibilité par les substrats. ...
416 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.
417 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
418 4lfy - Dihydroorotase from Bacillus anthracis and Staphylococcus aureus 2016 AJ Rice - 2016 - indigo.uic.edu 2.1 Introduction Class II DHOase from E. coli has been studied at length, producing many apo and complex crystal structures (Table I). The structure revealed DHOase is a homodimer zinc metalloenzyme Organism PDB Ligand Modification Burkholderia cenocepacia 4LFY Apo
419 3vab - Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis 2016 MG Peverelli, TPS da Costa, N Kirby - Journal of Biological , 2016 - ASBMB ... and 1TUF) (9), Aquifex aeolicus (PDB code 2P3E), and Brucella melitensis (PDB code 3VAB)show that ... both a dimer (PDB codes 1HKW and 1HKV) (7) and a tetramer (PDB code 2O0T ... arethe results of earlier studies aimed at characterizing the quaternary structure of DAPDC ...
420 4jpd - Dinmica molecular y consolidacin estructural de la frataxina humana 2016 SE Faraj - 2016 - ri.conicet.gov.ar The Alteration of the C-terminal Region of Human Frataxin Distorts its Structural Dynamics and Function Abajo: estructura de las protenas NB7804A de Bacillus halodurans ( PDB ID: 2KL4, amarillo); CyaY de Burkholderia cenocepacia ( PDB ID: 4JPD , gris), CyaY de
421 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
422 3u0g 4tvi, 4m0j Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold 2016 T Pavkov-Keller, GA Strohmeier, M Diepold- Scientific reports, 2016 - nature.com from Mycobacterium smegmatis 48 , 3UYY from Deionococcus radiodurans 49 , 3U0G from Burkholderia Crystallographic data processing and structure refinement statistics are presented in Table 4 confirmed function are D-amino acid aminotransferases (eg PDB -code: 1DAA
423 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
424 3ftp - Discovery of an L-Fucono-1, 5-Lactonase from cog3618 of the Amidohydrolase Superfamily 2012 ME Hobbs, MW Vetting, HJ Williams? - Biochemistry, 2013 - ACS Publications ... monomeric ensemble model generated by an overlay of the structures represented by PDB IDs Page 10 of 56 ACS Paragon Plus Environment ... Initial phases for unliganded BmulJ_04919 were determined by MR using MOLREP and a tetrameric search model (3FTP) (22). ...
425 4qtp - Discovery of antigens for early detection of Mycobacterium avium subsp. paratuberculosis and analysis of characteristics using bioinformatics tools. 2015 HT Park, HE Park, MK Shin, YI Cho - Korean Journal of , 2015 - search.ebscohost.com ... MAP MAP0380 coding anti-sigma factor antagonist protein(PDB ID: 4qtp,TM-score ... 1. Three-dimensional structure prediction using I-TASSER server. ... MAP1204p60 domain (PDB ID: 3i86, TM-score: 0.547), sequence identity 100 ...
426 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
427 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
428 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 ...
429 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...
430 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.
431 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
432 4gri 4g6z Dispensability of zinc and the putative zinc-binding domain in bacterial glutamyl-tRNA synthetase 2015 N Chongdar, S Dasgupta, AB Datta, G Basu - Bioscience reports, 2015 - bioscirep.org ... From extensive structural and sequence analyses from whole genome database of bacterialGluRS, we further show that in addition to many bacterial GluRS lacking a zinc-binding motif,the pZBD is actually deleted in some bacteria, all containing either glutaminyl-tRNA ...
433 3ue9 - Disruption of de novo ATP biosynthesis abolishes virulence in Cryptococcus neoformans 2016 R Blundell - 2016 - espace.library.uq.edu.au ... pioneered the concept of rational drug design (28) which involves the use of metabolic, genetica nd structural studies to identify potential targets, followed by the directed search ... AdSS has been purified and characterized from several sources ... Crystal structures are also available for the proteins from Homo sapiens (54%, PDB ID: 2V40); Mus musculus (54%, (50, 99)) ... and Burkholderia thailandensis (40%, PDB ID: 3UE9);. ...
434 3ftp 3f9i, 3grp Dissecting the structural elements for the activation of -ketoacyl-(acyl carrier protein) reductase from Vibrio cholerae 2016 J Hou, H Zheng, M Chruszcz - Journal of , 2016 - Am Soc Microbiol ... All enzymes in the active state (shown in gray with PDB accession numbers 1Q7B, 1UZN, 2C07, 2P68, 2UVD, 3FTP, 3LYL, 3OP4, 3RRO, 3OSU, and 4AFN) share the same open conformation in the cofactor binding site, while all the enzymes in the inactive state (shown in blue with PDB accession numbers 1I01, 1UZL, 2NTN, 3F9I, 3GRP, and 3TZC) have disordered ...
435 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
436 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),
437 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)
438 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
439 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
440 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
441 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
442 3pme - Double Receptor Anchorage of Botulinum Neurotoxins Accounts for their Exquisite Neurospecificity 2013 A Rummel - Botulinum Neurotoxins, 2013 - books.google.com ... Structural analysis of HCCD (3PME. pdb) exhibits a sialic acid binding site consisting of W1242, R1243 and F1244 homologous to that of BoNT/D. In conclusion, BoNT/A, B, E, F and G harbour a single GBS made up of the conserved amino acid motif E (Q) H (K) SXWY G ...
443 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 )
444 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
445 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
446 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
447 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
448 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
449 3md7 - Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cAMP and cGMP 2014 Y Tian, W Cui, M Huang, H Robinson, Y Wan - Biochemistry, 2014 - ACS Publications ... structure. The atomic model was built with O(39) and refined with REFMAC.(40). The yPDE1 structure was compared with structures in the Protein Data Bank by the online program Dali (http://www.ebi.ac.uk/Tools/structure/dalilite). ...
450 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.
451 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
452 2lol 2lky, 2kwl Dynamic Analysis of Backbone-Hydrogen-Bond Propensity for Protein Binding and Drug Design 2016 CA Menndez, SR Accordino - Biopolymers for , 2016 - crcnetbase.com ... binding (Bogan and Thorn 1998; Li and Liu 2009) propose that the structure of the ... layers of aset of complete (without missing residues) proteins without ligands (PDB IDs: 1AHO ... 2L4V, 2L5R,2L7W, 2LA1, 2LAO, 2LCU, 2LFN, 2LHC, 2LHS, 2LJM, 2LKB, 2LKY, 2LOL, 2LPK, 2PNE ...
453 3knu - Dynamics of substrate interactions in tRNA (m1G37) methyltransferase: Implications for drug discovery 2012 MK Palesis - 2012 - scholarscompass.vcu.edu ... The secondary structure of specific sequences is illustrated above the alignment. ... Page 29. 9 Figure6. Structural alignment of TrmD from different bacterial species: Anaplasma phagocytophilum(royal blue, PDB ID: 3KNU), Bartonella henselae (cyan, PDB ID: 31EF ...
454 4ex5 - Dynamics of the Active Sites of Dimeric Seryl t RNA Synthetase from Methanopyrus kandleri 2015 S Dutta, N Nandi - The Journal of Physical Chemistry B, 2015 - ACS Publications ... (j) Class II AsnRS (11AS.pdb) from Escherichia coli. (k) Class II LysRS (4EX5.pdb) of speciesBurkholderia thailandesis. ... The dimeric structure of SerRS from methanogenic Methanopyruskandleri ( mk SerRS) is interesting for the following reasons. ...
455 3l56 3khw, 3r2v Dynamique structurale et fonctionnelle du domaine C-terminal de la protine PB2 du virus de la grippe A 2015 E Delaforge - 2015 - tel.archives-ouvertes.fr ...Superposition des structures du 627-NLS de différentes souches sur 2VY6 en gris. A/little yellow-shouldered bat/Guatemala/060/2010 (H17N10) PDB 4WSB (vert), A/mexico/indre4487/2009 (H1N1) PDB 3KHW (orange), A/vietnam/1203/2004 (H5N1) PDB 3L56 (rose), A/Yokohama/2017/03 PDB 3R2V (H3N2) (bleu), ...
456 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 ...
457 3f9i - Education Corner 2014 J Beckham - Newsletter, 2014 - rcsb.org ... that organism that is essential for survival or virulence (eg fatty acid biosynthesis enzymes 3F9I, dihydrofolate reductases 3DAT, or host-pathogen signaling phosphatases 2Y2F). The students narrow their selection by those enzyme which have an available PDB crystal structure ...
458 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
459 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)
460 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
461 2kz0 - Effects of Mutating the PPAR Subfamily Specific Residueson Basal Dimerization with RXR 2012 KV Moore - 2012 - search.proquest.com entropy is the entropy distance for the subfamily, and the protein sequence position is the position of the amino acids found on model 2KZ0 of Protein Data Bank ( PDB ). Figure 1.1 Figure 2.2. Schematic Representation of the Domain Structure of PPARs. Page 25. 12
462 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. ...
463 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
464 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
465 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
466 3jst 4e98 Elucidation of genes of unknown function in alpha carboxysome operons: acRAF, BMVs and carbon regulatory PII proteins. 2014 NM Wheatley - 2014 - escholarship.org ... B) Structural alignment of acRAF to PCD from Toxoplasma gondii (PDB 2V6T). T. gondii PCD is colored green. C) Structural alignments of active sites among five PCDs shown in green (PDB IDs: 1DC0, 2EBB, 2V6T, 3JST, 4C45). acRAF is shown in magenta. ...
467 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
468 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
469 3f9i - Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2 S, 3 R, 4 S)-4-hydroxyisoleucine with three asymmetric centers 2017 X Shi, T Miyakawa, A Nakamura, F Hou, M Hibi- Scientific reports, 2017 - nature.com The structure of HILDH-NADH was determined using the molecular replacement method performed by the program MOLREP on the CCP4 suite using the structure of 3-ketoacyl-(acyl-carrier-protein) reductase (PDB code, 3F9I; sequence identity, 34%) as the initial model.
470 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
471 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
472 4xgi - Engineering, Predicting, and Understanding Nicotinamide Cofactor Specificity 2016 JKB Cahn - 2016 - thesis.library.caltech.edu geometries between homologues,11,12 and this structural diversity has limited the development of general methods PDB accession code use the cofactor from that protein and (m) denotes a structure of a mutant protein
473 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
474 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
475 4g50 - Entwicklung von Inhibitoren des macrophage infectivity potentiator -Proteins 2016 F Seufert - opus.bibliothek.uni-wuerzburg.de ... Zur Evaluierung möglicher struktureller Verbesserungen von S-1a wurden auch für BpMip Hot- Spot- und Docking-Analysen von M. Hein und M. Kuhn vorgenommen. Dazu wurden die Strukturen PDB 4G50 bzw. 4GGQ75 für BpMip und 2VCD-4 für LpMip verwendet.. ...
476 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.
477 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
478 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 ...
479 3pgz 3lgj ENZYME CONSTRUCT 2015 A Heron, J Clarke, R Moysey… - US Patent …, 2015 - freepatentsonline.com ... In order to assess whether a suitable protein structure exists to use as a “template” to build aprotein model, a search is performed on the protein data bank (PDB) database. ... The sequencealignment and template structure are then used to produce a structural model of the ...
480 3d53 3oc6 Enzyme repurposing of a hydrolase as an emergent peroxidase upon metal binding 2015 N Fujieda, J Schätti, E Stuttfeld, K Ohkubo, T Maier… - Chemical …, 2015 - pubs.rsc.org ... These wild-type proteins or their single mutant isoforms (pdb code: 3D53, 2F99, 1JSY, 1FHI(bearing a Q83E mutation), 1MEJ ... yellow sticks); (B) close-up view of the Cu1 binding site inCu·6-PGLac (PDB code 4TM7 ... The X-ray structure was refined to a resolution of 1.39 Å (Fig. ...
481 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
482 3ijp - Enzymology of bacterial lysine biosynthesis 2012 C Dogovski, SC Atkinson? - Biochemistry, Prof. Deniz Ekinci (Ed. ), ISBN: 978-953-51-0076-8, 2012 - cdn.intechopen.com ... 3.2 Structure of DHDPR 3.2.1 Subunit and quaternary structure of DHDPR The three-dimensional structure of DHDPR has been elucidated by X-ray crystallography from five diverse bacterial species, namely, Bartonella henselae, (PDB: 3IJP), E. coli (Scapin et al., 1995, 1997 ...
483 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
484 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
485 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
486 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...
487 3sds - Estructura - funcion - especificidad en el ambito de las transcarbamilasas: la putrescina transcarbamilasa 2012 P Ilacqua, L Mariano - 2012 - rodrigo.uv.es ... PCR: Reacci?n en cadena de la polimerasa (Polymerase Chain Reaction) PEG: Polietil?n glicol pfOTC: L-ornitina transcarbamilasa de Pyrococcus furiosus PDB: Banco de datos de prote?nas (Protein Data Bank) PTC: Putrescina transcarbamilasa Page 13. ...
488 4o5h 3i44, 3ek1, 4u3w, 4lih, 4o6r ESTUDO COMPUTACIONAL DA ENZIMA ALDEHYDE DEHYDROGENASE DE BIXA ORELLANA (URUCUM) E DOS LIGANTES ALDEÍDO DE BIXINA E NORBIXINA SOB A INFLUÊNCIA DO COFATOR NAD. 2017 Fábio Bruno Silva de Souza - ppgeq.propesp.ufpa.br Therefore, the 3D structure of the PDB Banco de Dados de Protenas (Protein Data Bank) RMN Ressonncia Magntica Nuclear FASTA Arquivo RCSB Site de investigao de Tecnologias para Bioinformtica Estrutural (Research Collaboratory for Structural Bioinformatics) G
489 3gka - Estudo estrutural das enzimas Topoisomerase II Mitocondrial e Old Yellow Enzyme de Trypanosoma cruzi 2014 NC Rodrigues - teses.usp.br ... resolution of 1.27 and 2.00 , respectively. The atomic coordinates and structure factors of the TcOYE structure in P212121 and P21 crystalline forms have been deposited in the Protein DataBank with the accession codes 4E2B and 4E2D, respectively. TcOYE displays a ...
490 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
491 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
492 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
493 3d53 - Estudos teóricos e estruturais para o desenvolvimento e síntese de aza-açúcares com atividade melhorada contra a Golgi α-manosidase II 2014 BPAC Pinto - 2014 - repositorium.sdum.uminho.pt ... Ao todo realizaram-se simulações de dinâmica molecular de 9 complexos GMII-ligando com os códigos PDB: 1HXK,2F1A,2OW6,3BLB,3DX4,3DDF,3D53,3EJU,3D4Y ...
494 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
495 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
496 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
497 3sdo - Evaluation of the Conformational Stability of Recombinant Desulfurizing Enzymes from a Newly Isolated Rhodococcus sp. 2016 F Parravicini, S Brocca, M Lotti - Molecular biotechnology, 2016 - Springer ... In this perspective, we built by homology a 3D model of DszA, whose crystallographic structurehas not been solved yet and ... against the Protein Data Bank (PDB) revealed that DszA sharesthe highest identity with a nitrilotriacetate monooxygenase (PDB code 3SDO.1.A ...
498 3sdw 3s5p, 4em8, 3qd5, 3sgw Evaluation of Trypanosoma brucei asparagine synthetase A and ribose 5-phosphate isomerase B as potential drug targets 2015 IMS Loureiro - 2015 - search.proquest.com ... Figure 9. Licensed current therapies against HAT. (A) Structures of drugs used to treat. early and late stage disease. ... PARP procyclic acidic repetitive protein. PDB Protein Data Bank. ... molecules with a conserved core structure of glycosylphosphatidylinositol (GPI) anchored. ...Coccidioides immintis (PDB 3QD5, 3SDW and 3SGW) (Min et al, 2002), Anaplasma phagocytophilum (PDB 4EM8), Clostridium thermocellium (PDB 3PH3, 3PH4 3HEE, and 3HE8) (Jung et al, 2011), Giardia lamblia (PDB 3S5P)
499 3s99 - Evidence for an ABC-Type Riboflavin Transporter System in Pathogenic Spirochetes 2013 RK Deka, CA Brautigam, BA Biddy, WZ Liu? - mBio, 2013 - Am Soc Microbiol ... bind a small molecule between its two lobes. An adenine-binding protein from Brucella melitensis (unpublished PDB accession code 3S99; RMSD = 1.8 ? over 260 comparable C ? atoms) is also structurally similar to TP0298. ...
500 3ujh - Evidence for Positive Selection within the PgiC1 Locus in the Grass Festuca ovina 2015 Y Li, B Canbäck, T Johansson, A Tunlid, HC Prentice - 2015 - dx.plos.org ... 0.45 Å root-mean-square deviations for the backbone atoms from the template Toxoplasma 3ujh.pdb structure. ... of the candidate sites in the homology-modeled PGIC1 3-D structure, it can ...For comparative purposes, the 3-D protein structural locations of the PGI amino acid sites ...
501 4ol9 - Evidence of kinetic cooperativity in dimeric ketopantoate reductase from Staphylococcus aureus. 2015 JE Sanchez, PG Gross, RW Goetze, RM Walsh… - Biochemistry, 2015 - ACS Publications ... the dimeric assembly of S. aureus KPR is conserved in the enzymes from Ralstonia eutropha, Ralstonia solanacearum, Mycobacterium tuberculosis, Enterococcus faecalis, Methylococcus capsulatus, and Bacillus subtilis (PDB entries 3HWR, 3GHY, 4OL9, 2EW2, 3I83, and 3EGO, respectively), despite low sequence identity ranging from 20−31% ...
502 4f4f 3v7n Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase 2017 G Kaur, S Subramanian- Cell Cycle, 2017 - Taylor & Francis ... Modeling of the spatial structure of eukaryotic ornithine decarboxylases. ... and H-group in SCOP (SCOP identifier 53685) 9 Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures . ...Table 1 PDB ID 4F4F A/B
503 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 . ...
504 3l56 - Evolutionary conservation of influenza A PB2 sequences reveals potential target sites for small molecule inhibitors 2017 H Patel, A Kukol - Virology, 2017 - Elsevier ... 2.2. Protein structure modelling. The PB2 sequence of a human H5N1 isolate, for which an N-terminal structural fragment ( PDB ID: 3L56 ) exists, was used to construct a full length structural model using the I-TASSER modelling server (Yang and Zhang, 2015; Zhang, 2008). ...
505 3o0m - Evolutionary coupling methods in de novo protein structure prediction 2016 S Seemayer - 2016 - edoc.ub.uni-muenchen.de On homomeric proteins, intermolecular couplings (red) have to be disentangled from intramolecular couplings (yellow) for de novo structure prediction to succeed (representative contacts mapped on PDB code 3O0M)
506 4g6z 4gri Evolutionary insights about bacterial GlxRS from whole genome analyses: is GluRS2 a chimera? 2014 S Dasgupta, G Basu - BMC evolutionary biology, 2014 - biomedcentral.com ... The structure shown on the left corresponds to the crystal structure of T. thermophilus GluRS (pdb ID: 1j09) with residues 1-322 and 323-468 comprising the N- and the C-terminal domains, respectively. Is GluRS2 a chimera? ...
507 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
508 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
509 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
510 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
511 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
512 3cez 3cxk Evolution of Structural and Coordination Features Within the Methionine Sulfoxide Reductase B Family 2014 E Shumilina, O Dobrovolska, A Dikiy - The Structural Basis of Biological , 2014 - Springer Figure V.2.2. Three-dimensional structure of Zn-binding site and thecorresponding regions of MsrBs family. For the explanation see text. A - MsrB1, M.musculus, 2KV1, [123]; B - MsrB1, H. sapience , 3MAO, not published; C - MsrB2, M.musculus, 2L1U, [125]; D - MsrB, X. campestris, 3HCI, [124]; E -B. pseudomallei,3CEZ/3CXK, not published; http://www.diva-portal.org/smash/get/diva2:603697/FULLTEXT02.pdf
513 3uam - Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases 2014 AJ Book, RM Yennamalli, TE Takasuka - Biotechnology for , 2014 - ncbi.nlm.nih.gov ... These are from Hypocrea jecorina (Trichoderma reesei, Protein Data Bank (pdb) id: 2VTC) [24], Thielavia terrestris (pdb id: 3EII) [7 ... pdb id: 2BEM) [25], Vibrio cholerae O1 biovar EI Tor (pdb id: 2XWX) [26], Burkholderia pseudomallei (pdb id: 3UAM), and Enterococcus faecalis ...
514 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
515 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
516 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
517 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 ...
518 3m1x 3gp3 Expanding molecular modeling and design tools to non-natural sidechains. 2012 D Gfeller, O Michielin, V Zoete - J Comput Chem. 2012 Jul 5;33(18):1525-35. Supplementary Figures 1JBO, 1KTP, 1PHN, 1QGW, 1XF6, 1XG0, 2BV8, 2C77, 2V8A, 2VJH, 2VJT, 3BRP, 3DBJ, 3O18, 3O2C
519 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.
520 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
521 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
522 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]
523 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
524 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
525 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
526 3qdf - Expression, purification, crystallization and preliminary crystallographic analysis of Cg1458: a novel oxaloacetate decarboxylase from Corynebacterium glutamicum 2011 T Ran, Y Wang, D Xu, W Wang - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2011 - scripts.iucr.org ... was collected at 1.9 ? resolution using synchrotron radiation on beamline BL17U of SSRF, Shanghai, China. Structure-solution attempts by molecular replacement were successful with PDB entries 3qdf or 2dfu as the template. ...
527 3oj7 - Expression, purification, crystallization and preliminary X-ray crystallographic analysis of human histidine triad nucleotide-binding protein 2 (hHINT2) 2013 R Dolot, A Wlodarczyk, GD Bujacz? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... above 15% similarity to a given hHINT2 sequence and BALBES, and five of them were used for further calculations: PDB entries 1kpf ... 404, 627-638.] ), 3oj7 (HIT family protein from Entamoeba histolytica; 40.2% similarity; Seattle Structural Genomics Center for Infectious Disease ...
528 3grk - Expression und Mutagenese von VEP1-kodierten Progesteron-5β-Reduktasen aus pharmazeutisch interessanten Angiospermen 2012 P Bauer - 2012 - opus4.kobv.de ... Parallel wurden mit Hilfe der „Superposition“-Funktion der Wincoot Software (II.2.5) in silico die Cosubstrat-Bindetasche der DlP5βR jeweils mit der von verschiedenen NADHabhängigen SDR-Enzymen überlagert (PDB: 2ztl, 3d3w, 3grk,..
529 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
530 3inn 4ed4 Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity 2014 T Krotzky, T Rickmeyer, T Fober… - Journal of chemical …, 2014 - ACS Publications ... To set up a more challenging task with respect to conformational and structural diversity, we ... serverPISCES of the Dunbrack lab(35) was employed, which kept only PDB structures that agreed ... thesequence identity does not exceed 25%, the method of structure determination is ...
531 3r2v - Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome 2013 S Warren, XF Wan, G Conant, D Korkin - PloS one, 2013 - dx.plos.org ...Table 3. Coverage and sequential similarity of protein templates. Template Template subtype Template similarity, % Residues covered 3R2V (A) H3N2 93 538-720
532 3fvb - Factors Controlling the Redox Potential of ZnCe6 in an Engineered Bacterioferritin Photochemical 'Reaction Centre' 2013 A Mahboob, S Vassiliev, PK Poddutoori, A van der Est? - PloS one, 2013 - dx.plos.org ... In addition, this aminoacid is conserved among ferritins from several organisms (PDB ID: 2FKZ, 3E1M, 3IS8, 3FVB) suggesting that it serves to regulate heme potential. Replacing it with an aliphatic residue is expected to eliminate this negative effect. ...
533 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
534 3moy - Fast and accurate computation schemes for evaluating vibrational entropy of proteins 2011 B Xu, H Shen, X Zhu, G Li - Journal of computational chemistry, 2011 - Wiley Online Library ... PDB id, Protein length, Standard NMA (kcal mol ?1 K ?1 ), Scaled BNM (kcal mol ?1 K ?1 ), Scaled GNM (kcal mol ?1 K ?1 ), Scaled ANM (kcal mol ?1 K ?1 ). 1al3, 324, 8.462, 8.405, 8.466, 8.818. ... 3m73, 314, 10.930, 10.912, 11.027, 10.248. 3moy, 263, 9.020, 9.108, 9.183, 9.171. ...
535 3laa 4g6c Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis 2014 K Opron, K Xia, GW Wei - The Journal of chemical physics, 2014 - scitation.aip.org ... The FRI is a solely structural based algorithm that does not reconstruct any protein inter- action ...the FRI prediction of protein B-factors does not require a stringently minimized structure and time ...The fFRI algorithm is developed by using appropriate data structures to avoid the ... TABLE V 3LAA 169 0.827
536 3ezo - Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering 2015 J Beld, DJ Lee, MD Burkart - Molecular BioSystems, 2015 - pubs.rsc.org ... from Helicobacter pylori), 3TQE (from Coxiella burnetii), 3PTW (from Clostridium perfringens),2QC3 (from Mycobacterium tuberculosis), 3EZO (from Burkholderia ... (d) The X-ray crystal structureof mechanistically crosslinked E. coli AcpP with FabA (PDB: 4KEH). ...
537 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
538 3eol - Filogenia molecular das enzimas isocitrato liase e malato sintase e sua evoluo em Viridiplanta 2014 RVM Almeida - 2014 - repositorio.ufrn.br ... Bayesian analysis). The identification of structural patterns in the evolution of theenzymes was made through homology modeling and structure prediction from proteinsequences. Based on comparative analyzes of in silico ...
539 4whx 3u0g First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for l-amino acids and R-amines 2016 KM Boyko, TN Stekhanova, AY Nikolaeva - Extremophiles, 2016 - Springer ... Secondary structure elements were assigned by DSSP (Touw et al. ... In the previously describedstructures of holo BCATs (PDB codes: 3U0G, 1I1K, 1WRV), the interdomain loop was found tobe ... 7) as well as in complexes of other BCATs (for example: 2EIY, 1IYE, 4WHX and 1I1L ...
540 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. ...
541 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
542 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
543 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
544 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
545 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
546 4xfj 4oh7 FreeSASA: An open source C library for solvent accessible surface area calculation 2016 S Mitternacht - arXiv preprint arXiv:1601.06764, 2016 - arxiv.org ... 88 PDB files were selected randomly from a set of size intervals ... PISCES specifies a specific chainin each structure, but in the following all chains were used, which resulted in the ... 4c1a, 4cj0, 4g6t,4g7x, 4gmu, 4h7u, 4kv7, 4la2, 4lix, 4n13, 4oh7, 4oxx, 4p0t, 4pj2, 4qas, 4xfj, 7odc. ...
547 4iv5 - From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases 2015 D Shi, NM Allewell, M Tuchman - International Journal of Molecular …, 2015 - mdpi.com ... dodecameric holoenzyme with DHOase, were determined [50,51]. Only one eukaryotic ATCasestructure, of Trypanosoma cruzi, has been determined (PDB code: 4IV5). ... Both domains havean αβα structure with a parallel β-sheet in the center and α helices on both sides. ...
548 3gvf - From Tilings to FibersBio-mathematical Aspects of Fold Plasticity 2014 C Lesieur, L Vuillon - 2014 - cdn.intechopen.com ... According to the PDB (Protein Data Bank [30] ) where all available atomic structures of proteins are stored ... x-ray structure of the cholera toxin B pentamer (CtxB5) is shown (PDB code 3CHB). ... Example with the protein 3GVF (PDB code), a D3 symmetry oligomer made of 6 chains ...
549 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
550 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) ...
551 3laa - Functional Analysis of the Polymorphic Membrane Protein Family of Chlamydia 2013 V Grinblat-Huse - 2013 - archive.hshsl.umaryland.edu ... The trimeric autotransporter adhesin head domain [RCSB indentifier 3LAA] from Burkholderia pseudomallei and the outer membrane adhesin/invasin [RCSB identifier 1K24] from Neisseria meningitidis were also used to attempt a structure prediction ...
552 3swo - Functional anatomy of complement factor H 2013 E Makou, AP Herbert, PN Barlow - Biochemistry, 2013 - ACS Publications ... Three-dimensional structures have been determined, in the settings of FH truncation fragments,for ... Low-resolution structural techniques were used to investigate intact FH (discussed below)and several FH fragments,(39, 42-45) but no three-dimensional structure of full ...
553 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. ...
554 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
555 3enk - Functional characterization and transcriptional analysis of galE gene encoding a UDP-galactose 4-epimerase in Xanthomonas campestris pv. campestris 2014 CT Li, CT Liao, SC Du, YP Hsiao, HH Lo… - Microbiological …, 2014 - Elsevier ... based on the detection of hydrogen bonds defined by an electrostatic criterion using the Dictionaryof Protein Secondary Structure database method obtained from PDBsum database. Thethree-dimensional structural model of Xcc GalE was based on E. coli GalE (PDB ID 1XEL ...B. pseudomallei (Bps-GalE, PDB code 3ENK); B. anthracis (Ban-GalE, PDB code 2C20); and T. thermophilus (Tth-GalE, PDB code 2P5U)...
556 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
557 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
558 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).
559 4f3p - Functional Diversity of Tandem Substrate-Binding Domains in ABC Transporters from Pathogenic Bacteria 2013 F Fulyani, GK Schuurman-Wolters, AV Zagar, A Guskov… - Structure, 2013 - Elsevier Supplemental Information ... unliganded liganded 1 42 glnH Escherichia coli Gln v v 1.94 1GGG, 1WDN 0.5 µM (Hsiao, et al., 1996) 2 38 glnH Burkholderia pseudomallei Gln v 2.4 4F3P nd Abendroth J, 2012 ...
560 4dlp - Functional effect of alterations to E. coli methionyl-trna synthetase -linker length 2015 Y Xia - 2015 - search.proquest.com ... Table 2. Crystal structure of MetRS with different ligands. Organism Ligand PDB id Reference E. coli No ligand 1QQT 2. E. coli Methionine 1F4L 40. E. coli Methionine phosphonate 1P7P 41. ... A. aeolicus tRNAMet 2CSX 11. B. melitensis Selenomethionine 4DLP 42. ...
561 4dhk 3km3 Functional Exploration and Characterization of the Deaminases of Cog0402 2014 DS Hitchcock - 2014 - oaktrust.library.tamu.edu ... Page 29. 18 4DHK). The catalytic machinery for both of these reactions remains intact. Substrate ...centered around residues aligning to the catalytic Glu138. However the structure shows 370AAs, whereas E. coli dCTP deaminase (PDB: 1XS1) is only 193 residues. A full ...
562 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 ). ...
563 3glq - Functional Prediction of Binding Pockets 2012 M Kontoyianni, CB Rosnick - Journal of chemical information and modeling, 2012 - ACS Publications ... The dataset was compiled using the protein databank, the Structural Classification of Proteins (SCOP),68 the Enzyme Classification (EC)69 system and the Washington University Basic Local Alignment Search Tool Version 2.0 (WU- ...
564 3dms - Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases 2012 R Vinekar, C Verma, I Ghosh - BMC , 2012 - bmcbioinformatics.biomedcentral. ... The current study therefore concentrates mainly on dimeric NADP-dependent IDHs from subfamilies I and II and additionally subfamily IV (Table 1), with an emphasis on regulation in dimeric M.tb IDH. Burcholderi apseudomallei BpIDH Q63WJ4_BURPS 3DMS. ...
565 4qtp - Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets 2016 A Gazi, MG Kibria, M Mahfuz, R Islam, P Ghosh - Gene, 2016 - Elsevier ... Conformational B cell epitopes of NP_216420.1 (UniProt ID: O07728) predicted from the 3D structure template under PDB ID 4QTP (Crystal structure of an anti-sigma factor antagonist from M. paratuberculosis). ...
566 4ed9 - Function and X-Ray crystal structure of Escherichia coli YfdE 2013 EA Mullins, KL Sullivan, TJ Kappock - PloS one, 2013 - dx.plos.org ... the same orientation as Figure 4B. PDB entries are 4hl6 (white), 4ed9 (dark blue), 1p5h (green) [69], 1pt7 (cyan) [24], 3ubm (orange) [25], 1*k7 (yellow) [70], 1*74 (magenta) [71], and 2g04 (pink) [72]. (B) ML phylogram of the ...
567 3meq - Furfural reduction mechanism of a zinc-dependent alcohol dehydrogenase from Cupriavidus necator JMP134 2012 CH Kang, R Hayes, EJ Sanchez, BN Webb? - Molecular Microbiology, 2012 - Wiley Online Library ... through the coordinates of ADH from Brucella melitensis (3MEQ). Iterative model building and refinement took place using the programs coot (Emsley et al., 2010) and phenix (Adams et al., 2010). All FurX coordinates have been deposited in the Protein Data Bank: 3S1L (apo ...
568 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
569 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
570 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),
571 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
572 3ixc 3oi9, 3mxu, 3laa, 3mdx, 3m1x, 3lqw General Method for Designing Self-Assembling Protein Nanomaterials 2013 D Baker, N King, W Sheffler, T Yeates - US Patent App. 13/802,464, 2013 - Google Patents ... subunits. The wild-type protein from which O3-33 was derived (PDB ID 3N79) did not assemble to a higher order structure; it eluted from the column mostly as trimers, with a small peak corresponding to a dimer of trimers. Analytical ...
573 4qic - General Stress Signaling in the Alphaproteobacteria 2015 A Fiebig, J Herrou, J Willett - Annual review of genetics, 2015 - annualreviews.org ... (f) Structural representation of full-length PhyR in an open conformation bound to NepR(PDB:4QIC). This complex structure evinces an unusual exchange of receiver domain secondaryelements 5-12 (yellow) between adjacent PhyR/NepR complexes in the crystal lattice. ...
574 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),
575 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
576 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.
577 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
578 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
579 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
580 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,
581 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
582 3kc6 - Genomic Signatures for Avian H7N9 Viruses Adapting to Humans 2016 GW Chen, SM Kuo, SL Yang, YN Gong, MR Hsiao - PloS one, 2016 - journals.plos.org ... because it is the latest and the only full-length PB2 being resolved thus far [44], comparing withthe other commonly used avian influenza H5N1 PB2 C-terminal domain (CTD) structure (PDBID 3KC6) of 204-aa long covering only positions 538 to 741 of a full-length PB2 protein. ...
583 4lgv - Glicose 6-fosfato desidrogenase como alvo molecular para desenvolvimento de frmacos: estudos estruturais e identificao de inibidores 2016 GF Mercaldi - 2016 - repositorio.unicamp.br ... Comparison of this structure with the human homologous enzyme Page 10. ... contribute to improve the structural and functional knowledge about the G6PDHs, an enzyme ... A) Orientao do substrato na estrutura do complexo ternrio ( PDB 5AQ1) obtido pelo nosso grupo. ...
584 3k2h - Global optimization-based inference of chemogenomic features from drug–target interactions 2015 S Zu, T Chen, S Li - Bioinformatics, 2015 - Oxford Univ Press ... In recent years, several non-structure-based methods, which are not limited by the structureinformation have been developed, along the ... Examples of the substructure-domain interactionsvalidated from the PDB database: (A) PDB entry 1u70, (B) PDB entry 3k2h, (C) PDB ...
585 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
586 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
587 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
588 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
589 3tmg - Glycine Betaine Recognition through Cation-PI Interactions in Crystal Structures of Glycine Betaine Complexes with C-Ethyl-pyrogallol [4] arene and C-Ethyl-resorcin [4]arene as Receptors 2013 I Fujisawa, K Aoki - Crystals, 2013 - mdpi.com ... 18. Gardberg, A.; Fox, D.; Staker, B.; Stewart, L. Crystal Structure Of Glycine Betaine, L-Proline ABC Transporter, Glycine/Betaine/L-Proline-Binding Protein (ProX) from Borrelia Burgdorferi;PDB (Protein Data Bank): Upton, NY, USA, 2013; No. 3TMG. 19. ...
590 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
591 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
592 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
593 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 )
594 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
595 3laa - Haemophilus influenzae surface fibril (Hsf) is a unique twisted hairpin-like trimeric autotransporter 2014 B Singh, T Al Jubair, M Mörgelin, A Sundin… - International Journal of …, 2014 - Elsevier ... The templates are presented as Hsf amino acids (PDB code of template: identity/similarity, gap),0136 ... 1863–2023 (1s7m: 73/79, 3), 2024–2143 (2qih: 11/23, 0), 2144–2315 (3laa: 15/22 ... A domain close to the C-terminal (2144–2315 aa) was constructed from PDB:3laa with low identity, but having a high local similarity. ...
596 3sdo - Halogen bonding at the ATP binding site of protein kinases: Preferred geometry and topology of ligand binding 2013 J Pozna?ski, D Shugar - Biochimica et Biophysica Acta (BBA)-Proteins and ?, 2013 - Elsevier ... bonding mode occurs to the p-loop region (Arg43-Phe54 in CK2?) in 1 J91, 1ZLT, 2GU8, 2UW8, 2X6D 3NGA 3SDO, frequently accompanying ... Thus, the side-chain carboxyl of Asp (PDB IDs: 1ZOH, 3KXG, 1Q4L, 1FVT, 1UV5, 3ZZ2), a backbone carbonyl of Gly (PDB IDs: 2XP2 ...
597 4xfj - HELICAL PARAMETERS OF REGULAR π-HELICES IN PROTEINS (Part 2) 2016 D. Batkhishig, B. Mijiddorj, P. Enkhbayar, 2016 - cyberleninka.ru to the DSSP program that is dedicated to identifying n-helices, which were seldom assigned by older versions of DSSP and STRIDE [7]. The secondary structure assignment methods 4XFJ A_68-74 PDB ID Chain_Po sition P (A) n Az (A)b r (A) Vc (A3) P (A) Identified Program
598 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
599 3i0p - Helix?helix interactions and their impact on protein motifs and assemblies 2010 N Kurochkina - Journal of Theoretical Biology, 2010 - Elsevier ... Protein, Source, PDB designation. Four-?-helix bundle, Myohemerythrin, Thermiste zostericola, 2 mhr. Hemerythrin, Thermiste discrita, 2hmq. ... Aeropyrum pernix, 2d4a. Entamoeba hystolitica,3i0p. Uridine-diphosphate-galactose 4-epimerase, Trypanosoma brucei, 1gy8. ...
600 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
601 3d64 - Hidden Relationship between Conserved Residues and Locally Conserved Phosphate-Binding Structures in NAD (P)-Binding Proteins 2012 CY Wu, YH Hwa, YC Chen, C Lim - The Journal of Physical Chemistry, 2012 - ACS Publications ... Bank (PDB).2 In the absence of structural data, sequence similarity search tools are useful in annotating protein function and in aiding the design of experiments for further studies. ... the NAD(P)-binding domains in the current PDB. ...
602 3js4 - Highly Active Yeast MnSOD has a Novel Mechanism Involving Six-coordinate Mn (3+) Species 2012 Y Sheng - 2012 - escholarship.org ... The enzyme structures of four classes of SOD. (A) Homo sapien CuZnSOD (pdb code: 1PU0); (B) Streptomyces coelicolor NiSOD (pdb code: 1T6U); (C) Saccharomyces cerevisiae MnSOD (pdb code: 3LSU); (D) Anaplasma phagocytophilum FeSOD (pdb code: 3JS4). Page 22. ...
603 3enk - Highly selective l-threonine 3-dehydrogenase from< i> Cupriavidus necator</i> and its use in determination of l-threonine 2011 T Ueatrongchit, Y Asano - Analytical Biochemistry, 2011 - Elsevier ... BaGluE, UDP-glucose 4-epimerase from Bacillus anthracis (2C20); BpGluE, UDP-glucose 4-epimerase from Burkholderia pseudomallei (3ENK); SvDHT, DTDP-glucose 4,6-dehydratase from Streptomyces venezuelae (1R66); ...
604 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
605 3eiz 3i4t High pKa variability of cysteine residues in structural databases and the effect of H-bond contributions 2014 SM Marino, İ Soylu - Türk Biyokimya Dergisi [Turkish Journal of …, 2014 - turkjbiochem.com ... High pKa variability of cysteine residues in structural ... RESULTS of ppka3 on PDB-crystal datasetprot=protein name res_num=residue number H-bond=hydrogen bond contribution to pKaprediction (pKa) Coul=electrostatics (from Coulombic interactions) contribution to pKa ...
606 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
607 3swo 3sf6 High-resolution structures of cholesterol oxidase in the reduced state provide insights into redox stabilization 2014 E Golden, A Karton, A Vrielink - Acta Crystallographica Section D: …, 2014 - scripts.iucr.org ... This state also shows the presence of multiple conformations of the aromatic triad residues whichwere not observed in the aerobic 2-propanol structure. ... Proc. Natl Acad. Sci. USA, 111, 3389-3394.] ;PDB entries 3swo and 3sf6 (Seattle Structural Genomics Center for ...
608 3glq 3n58 High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus) 2012 K Brzezinski, Z Dauter, M Jaskolski - Acta Crystallographica Section D Biological Crystallography, 2012 - scripts.iucr.org ... Protein Sci. 17, 2134-2144.] ), Burkholderia pseudomallei (PDB entry 3glq ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Brucella melitensis (PDB entry 3n58 ; Seattle Structural Genomics Center for Infectious Disease, unpublished work). ...
609 3uk1 3upt High-resolution structures of Lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate 2015 P Lukacik, CMC Lobley, M Bumann - Section F: Structural , 2015 - scripts.iucr.org ... In this work, we present high-resolution crystal structures of the L. salivarius UCC118 Tkt protein(LsTktA) in the presence and absence ... Burkholderia thailandensis (PDB entry 3uk1 ), B. pseudomallei (PDB entry 3upt ), ...
610 3ek2 3k31, 3k2e High-resolution structures of Thermus thermophilus enoyl-acyl carrier protein reductase in the apo form, in complex with NAD+ and in complex with NAD+ and triclosan 2012 JM Otero, AJ Noel, P Guardado-Calvo? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... 3f4b ; M. Yu et al., unpublished work) and the bacteria Aquifex aeolicus (PDB entry 2p91 ; Southeast Collaboratory for Structural Genomics and RIKEN Structural Genomics/Proteomics Initiative, unpublished work), Burkholderia pseudomallei (PDB entry 3ek2 ; Seattle Structural ...
611 3p96 - High Throughput Screen Identifies Small Molecule Inhibitors Specific for Mycobacterium tuberculosis Phosphoserine Phosphatase 2014 G Arora, P Tiwari, RS Mandal, A Gupta - Journal of Biological Chemistry, 2014 - ASBMB ... not available. The closest homolog for SerB2 protein was SerB protein from Mycobacterium avium (Protein Data Bank code 3P96) with 84% sequence identity, 99% query coverage, and an E value of 0.0. The superimpositions ...
612 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 ...
613 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
614 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
615 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
616 5dxd - HOMOLOGY MODELING AND STRUCTURAL STUDIES OF CELL WALL BINDING PROTEIN -1, 3, GLUCANASE FROM NEUROSPORA CRASSA 2017 KA Kumar, SK Gousia, MM Moses, JNL Latha - ejpmr.com 5dxd .1.A 17.97 monomer HHblits X-ray 1.70 0.29 0.30 Putative beta-glucanase normalized QMEAN score (0.40) and protein size in non-redundant set of PDB structures in the and Schwede, T. Toward the estimation of the absolute quality of individual protein structure models
617 3men - Homology modeling of parasite histone deacetylases to guide the structure-based design of selective inhibitors 2015 J Melesina, D Robaa, RJ Pierce, C Romier - Journal of Molecular , 2015 - Elsevier ... Wizard (Schrdinger Inc.) by adding hydrogen atoms, defining the protonation states of residuesand minimising the structure to remove steric ... Number, Organism/protein name, Abbreviation,PDB ID. ... 10, Burkholderia pseudomallei acetylpolyamine aminohydrolase, BpAPAH, 3MEN ...
618 3nrr 3i3r Homology modeling, vasorelaxant and bradykinin-potentiating activities of a novel hypotensin found in the scorpion venom from Tityus stigmurus 2015 RJA Machado, LGM Junior, NKV Monteiro… - Toxicon, 2015 - Elsevier ... thymidylate synthase from B. bovis with dUMP, Ralitrexed and NADP (PDB ID: 3NRR, ChainA ... Protein Data Bank are listed here in increasing order of identity: X-ray structure dihydrofolatereductase/thymidylate synthase from B. bovis at 2.35 Å resolution (PDB ID: 3I3R ...
619 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
620 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])
621 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
622 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
623 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
624 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
625 3gvg - How proteins work 2011 M Williamson - 2011 - books.google.com ... in structure motifs 24 Membrane proteins are different from globular proteins 29 The structureofa protein is (more or less) determined by its sequence 31 Some proteins form metastablestructures 32 Structure is conserved more than sequence 33 Structural homology can be ...
626 3ecd - How pyridoxal 5'‐phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state 2015 G Giardina, P Brunotti, A Fiascarelli, A Cicalini… - FEBS …, 2015 - Wiley Online Library ... shows a completely open conformation of the dimer (PDB id: 3ecd), as in the case of apo-SHMT2 ...method using the apo-enzyme (PDB: 3ou5) as search model in MOLREP [54 ... F, Morea V,Angelaccio S, Saccoccia F, Contestabile R & Ilari A (2014) The crystal structure of archaeal ...
627 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
628 4h3z 4odj How to fold intricately: using theory and experiments to unravel the properties of knotted proteins 2017 SE Jackson, A Suma, C Micheletti - Current Opinion in Structural Biology, 2017 - Elsevier ... Despite the early evidence of a shallowly knotted carbonic anhydrase structure [1 and 2], the ...Homodimeric entries 3BJX and 4H3Z are accordingly represented by chains B instead of thedefault ... The complete list of knotted PDB entries, including a few where knots are likely ...
629 4dz6 - How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer 2017 GM Blackburn, J Cherfils, GP Moss- Pure and Applied, 2017 - degruyter.com Architecture and Design Arts Asian and Pacific Studies Business and Economics Chemistry Classical and Ancient Near Eastern Studies Computer Sciences Cultural Studies Engineering General Interest Geosciences History Industrial Chemistry Islamic and Middle Eastern
630 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 Check Out. Menu: Subjects: Architecture and Design; Arts; Asian and Pacific Studies; Business and Economics; Chemistry; Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008) by Brecher, Jonathan; Measurement of cellulase
631 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. ...
632 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.
633 3nrr - Human Dihydrofolate Reductase and Thymidylate Synthase form a complex in vitro and co-localize in normal and cancer cells 2016 A Antosiewicz, A Jarmua, D Przybylska - Structure and , 2016 - Taylor & Francis ... (Konagurthu, Whissto Stuckey, & Lesk, 2006). The AB dimer of the human TS structure 1HVY(Phan et al., 2001) and monomer A of the DHFR structure 1KMS (Klon et al., 2002) ... PDB ID: 3NRR)(Begley et al., 2011), Cryptosporidium hominis (Ch; PDB ID: 1QZF) ...
634 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
635 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
636 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
637 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.
638 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).
639 3slg - Human UDP-?-d-xylose Synthase and Escherichia coli ArnA Conserve a Conformational Shunt That Controls Whether Xylose or 4-Keto-Xylose Is Produced 2012 SJ Polizzi, RM Walsh Jr, WB Peeples, JM Lim? - Biochemistry, 2012 - ACS Publications ... Recently, the Seattle Structural Genomics Center for Infectious Disease deposited the atomic coordinates of an annotated UGA decarboxylase from Burkholderia pseudomallei (PDB entry3SLG) which conserves the same proline packing surface associated with the ...
640 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
641 4oj7 - Identificao de protenas exclusivas de fitopatgenos da famlia Xanthomonadaceae: uso de genmica comparativa para identificao de novos alvos de combate. 2016 RAB Assis - 2016 - repositorio.ufop.br Pro Prolina Ser Serina Thr Treonina Phe Fenilalanina Trp Triptofano Tyr Tirosina CAZy Carbohydrate active enzyme PDB Protein Data Bank Page 14. X RESUMO A famlia Xanthomonadaceae compreende espcies diferentes de proteobactrias no
642 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
643 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
644 4oj7 - Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the 2017 R de AB Assis, LC Polloni, JSL Patan, S Thakur- Scientific reports, 2017 - nature.com Based on this functional analogy, we performed a detailed in silico analysis of the CM-sec three-dimensional (3D) structure. The hit in the structural analysis was from Burkholderia thailandensis (PDB 4oj7.1.A) with 98.2% coverage and 39.74% identity, confirming the typical CM domain fold
645 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
646 3qi6 - Identification and Characterization of a Methionine γ‐Lyase in the Calicheamicin Biosynthetic Cluster of Micromonospora echinospora 2015 H Song, R Xu, Z Guo - ChemBioChem, 2015 - Wiley Online Library ... with iMOSFILM, and scaled with SCALA (CCP4 suite).35 The initial search model was generatedby pruning non-conserved residues of the Mycobacterium ulcerans cystathionine γ-synthase(MetB; PDB ID: 3QI6) with CHAINSAW.36 The structure of CalE6 was ...
647 3oib - Identification and characterization of cholesterol metabolism related genes and gene products from Mycobacterium tuberculosis 2015 M Yang - 2015 - search.proquest.com ... Cholesterol has indispensible structural and regulatory roles in humans. ... N-terminis. C-terminus.Figure 2-1. Typical human homotetrameric ACAD structure. (a) Homotetrameric assembly of.human MCAD (PDB code: 1EGC) with four FAD molecules (yellow spheres) and four. ...
648 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
649 3iml 3n58 Identification and Characterization of the Chlamydia trachomatis L2 S-Adenosylmethionine Transporter 2011 R Binet, RE Fernandez, DJ Fisher, AT Maurelli - mBio, 2011 - Am Soc Microbiol ... The alignment was generated using the Tcoffee expresso Web server using Arabidopsis thaliana MAT1 sequence (P23686) and the tertiary sequence of rat MAT1 (PDB ID 1O9T), E. coli MAT (PDB ID 1XRC) and Burkholderia pseudomallei MAT (PDB ID 3IML). ...
650 3lg6 - Identification and clarification of the role of key active site residues in bacterial glutathione< i> S</i>-transferase zeta/maleylpyruvate isomerase 2011 T Fang, DF Li, NY Zhou - Biochemical and Biophysical Research Communications, 2011 - Elsevier ... 2. Phylogenetic relationships of NagL (PDB ID, 2JL4) and other representative cGSTs from the protein data bank. ... delta (1V2A, 1R5A, 3F6F, 3EIN, 1PN9, 1JLV, 3F63 and lJLW), omega (1EEM), tau (2VO4, 1OYJ and 1GWC) and zeta (1FW1, 1E6B, 2JL4, 3NIV, 3LG6 and 2CZ2). ...
651 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
652 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
653 3p10 - Identification and structural characterization of two 14-3-3 binding sites in the human peptidylarginine deiminase type VI 2012 R Rose, M Rose, C Ottmann - Journal of Structural Biology, 2012 - Elsevier ... of structures ( [Schumacher et al., 2010a], [Schumacher et al., 2010b] and [Molzan et al., 2010]) (PDB IDs: 3NKX, 3O8I, 3IQV, 3LW1, 3IQU, 3IQJ, 3P10, 3P1Q, 3P1N, 3P1R, 3P1S, 3MHR), and which only yields crystals when a peptide is bound in the binding groove of 14-3-3 ?. ...
654 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
655 3hgb - Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens 2015 JGM Rack, R Morra, E Barkauskaite, R Kraehenbuehl… - Molecular cell, 2015 - Elsevier ... SpyGcvH-L structure is shown in black and canonical GcvH of cattle (PDB: 3KLR), pea (PDB: 1DMX), and M. tuberculosis (PDB: 3HGB) in orange, green, and yellow, respectively. Residue numbers for GcvH-L are given. ...
656 3qh4 - Identification of amino acids related to catalytic function of Sulfolobus solfataricus P1 carboxylesterase by site-directed mutagenesis and molecular modeling 2016 YH Choi, YN Lee, YJ Park, SJ Yoon, HB Lee - BMB reports, 2016 - ncbi.nlm.nih.gov ... the basis of the Protein Data Bank (PDB) databases reported previously: AfuEst (PDB code: 1jji ...esterase (1qz3), MetEst (2c7b), StoEst (3aik), Mycobacterium marinum esterase (3qh4), PcaEst(3zwq ... was created by homology modeling as the superimposed ribbon structure onto it ...
657 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
658 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
659 3qbp - Identification of a novel fumarase C from Streptomyces lividans TK54 as a good candidate for l-malate production 2014 RR Su, A Wang, ST Hou, P Gao, GP Zhu? - Molecular Biology Reports, 2014 - Springer ... The structure files of fumarases from Mycobacterium marinum (MmFum, PDB code: 3QBP) and Mycobacterium tuberculosis (MtFum, PDB code: 3NO9) were downloaded from the PDB web site (http://?www.?rcsb.?org/?pdb/?). Results and discussion. ...
660 3p96 - Identification of a novel ligand binding site in phosphoserine phosphatase from the hyperthermophilic archaeon Thermococcus onnurineus 2013 TY Jung, YS Kim, BH Oh, E Woo - Proteins: Structure, Function, and Bioinformatics, 2013 - Wiley Online Library ... Flexible movement between the open structure (PDB ID: 1L8L, 1RKV, 2FEA, and 3M1Y), colored in bright orange, and closed structures (PDB ID: 1F5S, 1L7M, 1J97, 1L7P, 3P96, and 3KD3), colored in bluewhite, were analyzed by the program DynDom. ...
661 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
662 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
663 3gmt - Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches 2011 D Armenta-Medina, E P?rez-Rueda? - Proteins: Structure, Function, and Bioinformatics, 2011 - Wiley Online Library ... PDB ID, Organism, Resolution ?, Chain, %ID. 4ake, Escherichia coli, 2.20, A, 100. 3be4, Cryptosporidium parvum, 1.60, A, 45. 3fb4, Marinibacillus marinus, 2.00, A, 49. 3gmt, Burkholderia pseudomallei, 2.10, B, 66. 2c9y, Homo sapiens, 2.10, A, 49. 1ak2, Bos taurus, 1.92, A, 48. ...
664 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
665 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)
666 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
667 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
668 2khr - Identification of outer membrane and exoproteins of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae 2015 AJ Brinkworth, CH Hammer, LR Olano, SD Kobayashi- PloS one, 2015 - ncbi.nlm.nih.gov are based on template proteins that have been submitted to the RCSB protein database as crystal structure or NMR data ID, Protein, Length (aa), 1 st Hit PDB , Protein Template, Conf, Id, 2 nd Hit PDB , Template, Conf G8VZH0, Hyp, 1007, 2bcm, DaaE adhesin, 31, 25, 2khr , MbtH
669 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
670 3p0x - Identification of protein-ligand binding site using machine learning and hybrid pre-processing techniques 2015 YKG Wong - 2015 - ira.lib.polyu.edu.hk ... This type is suit- able if no structural information about the target is available. Another one isstructure- ... All this information can be found from the Protein Data Bank (PDB) [6] or Protein Qua-ternary Structure file server (PQS) [7], which show the atomic coordinates and the qua- ...
671 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
672 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
673 3d53 3ome Identification of two-histidines one-carboxylate binding motifs in proteins amenable to facial coordination to metals 2012 M Schmid, G Collet, P Cuniasse, F Gilardoni? - Metallomics, 2012 - pubs.rsc.org ... 60% sequence similarity are indicated by a * PDB code, Annotated protein function, Carboxylate, Histidine 1, Histidine 2. ... Aminocarboxypropyl-transferase, Glu86*, His193*, His195*. 3D53, Pyrophosphatase, Asp114*, His76*, His77*. ...
674 4ed9 - Identifying functionally important cispeptide containing segments in proteins and their utility in molecular function annotation 2014 S Das, S Ramakumar, D Pal - FEBS Journal, 2014 - Wiley Online Library ... dots. (G), (H) and (I) depict the presence of a functionally important fragment from 1bxrA (carbamoyl phosphate synthetase) in 4ed9A (CAIB/BAIF family protein), an unknown function protein. ...
675 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
676 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
677 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
678 2khp - Identifying selective ligands for glutaredoxin proteins with fragment based drug design approach and optimization of the bacterial selective hits 2016 RB Khattri - 2016 - etd.ohiolink.edu ...These were compared to structures deposited in the Protein Data Bank (RCSB PDB). The PBD name for the BrmGRX is 2KHP (Leeper et. al, 2011) and hGRX1 is 1JHB (Sun et. al, 1998).. ...
679 4f2n - Imidazole-containing phthalazine derivatives inhibit Fe-SOD performance in Leishmania species and are active in vitro against visceral and mucosal leishmaniasis 2015 M Sánchez-Moreno, F Gómez-Contreras… - Parasitology, 2015 - Cambridge Univ Press .. The Fe-SOD enzymes structure were obtained from the Brookhaven protein data bank (entry 2gpc for Trypanosoma cruzi and entry 4F2N for Leishmania, corresponding to L. major, as it is the only published structure for a Leishmania species) and their energies were minimized ...
680 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
681 3gka 3r20, 4die, 3nxs, 3tk1, 4kam, 3md0 Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design 2016 C Ehrt, T Brinkjost, O Koch - Journal of medicinal chemistry, 2016 - ACS Publications ... of 3D structures of proteins and protein ligand complexes is one prerequisite for rational structure-based drug design that deals with the utilization of these structural data to ... Figure 1. PDB statistics on the number of released PDB entries (blue bars) and the number of new ...
682 3obk - Impact of quaternary structure dynamics on allosteric drug discovery 2013 EK Jaffe - Current topics in medicinal chemistry, 2013 - ingentaconnect.com ... Toxoplasma gondii PBGS (PDB id 3OBK, shown left) contains a 13 amino acid C-terminal exten- sion that forms a domain swapped beta sheet (orange/yellow), which locks the dimer into the pro-octamer conformation. Pseudomonas ...
683 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
684 3i4e - Importance of the Clr2 protein in heterochromatin formation in the fission yeast Schizosaccharomyces pombe 2017 D Steinhauf - 2017 - diva-portal.org ... The exact function of Clr2 is unknown but the 3D crystal structure of Clr2 reveals four distinct domains; an N-terminal domain ... The second internal domain resembles a bromo-adjacent homology (BAH) domain, and 3D- structures show the domain interacting with Clr1 through a ... Finally, the Isocitrate Lyase (PDB entry: 3I4E) was used for the modeling of C2SM3.
685 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
686 3gvc - Improved xylitol production by expressing a novel D-arabitol dehydrogenase from isolated Gluconobacter sp. JX-05 and co-biotransformation of whole cells 2017 X Qi, H Zhang, TA Magocha, Y An, J Yun, M Yang - Bioresource , 2017 - Elsevier ... Phyre2 (Kelley et al., 2015) was used to predict the 3D structure of ArDH. ..Another two SDR enzymes, short-chain dehydrogenase reductase (PDB ID: 3GVC) of M. tuberculosis and galactitol dehydrogenase (PDB ID: 2WSB) of R. sphaeroides were also used in the superposition of structure modeling. ...
687 3uam - Improving extracellular production of Serratia marcescens lytic polysaccharide monooxygenase CBP21 and Aeromonas veronii B565 chitinase Chi92 in 2017 Y Yang, J Li, X Liu, X Pan, J Hou, C Ran, Z Zhou - AMB Express, 2017 - Springer ... 2012), Chitin Binding Domain from Burkholderia pseudomallei ( PDB ID: 3UAM ) and CBP ... PubMedCentralGoogle Scholar. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and ...
688 3r8c 3te8 Improving ranking of models for protein complexes with side chain modeling and atomic potentials 2013 S Viswanath, DVS Ravikant? - Proteins: Structure, Function, and Bioinformatics, 2012 - Wiley Online Library ... Target PDB ID, Receptor homolog (PDB_chain): target receptor chain, Ligand homolog (PDB_chain): target ligand chain. 2xt4, 2XT2_A:B, 2XT2_A:A. 2xty, 2XTW_A:B, 2XTW_A:A. ... 3pra, 3PRB_A:B, 3PRB_A:A. 3r8c, 3R20_A:A, 3R20_A:B. 3rd6, 3Q64_A:A, 3Q64_A:B. ...
689 3v8h - Inactivation of the Thymidylate Synthase thyA in Non-typeable Haemophilus influenzae Modulates Antibiotic Resistance and Has a Strong Impact on Its 2017 I Rodrguez-Arce, S Mart, B Euba- Frontiers in cellular, 2017 - journal.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 ...
690 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
691 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 :
692 3dms - Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase 2012 S Gon?alves, SP Miller, MA Carrondo, AM Dean? - Biochemistry, 2012 - ACS Publications ... To date, there are 27 crystal structures of E. coli isocitrate dehydrogenase in the Protein Data Bank (Table 3). Burkholderia pseudomallei Strain 1710b (UNIPROT Q3JV82), 74.2% identity 3dms 71 1.65 2011 0.92 0.62 ...
693 3glq - Inexpensive method for selecting receptor structures for virtual screening 2015 Z Huang, CF Wong - Journal of chemical information and modeling, 2015 - or.nsfc.gov.cn ... 1LI4, 1V8B, 1XWF, 2H5L, 2ZIZ, 2ZJ0, 2ZJ1, 3CE6, 3D64b, 3DHY, 3G1U, 3GLQ, 3H9U, 3N58 ...the results for docking 152 actives and 9942 decoys to 36 crystal structures for BRAF. For thissystem, the SPI identified the best structure (PDB id 3IDP) for virtual screening as the other ...
694 3eiz - Influence of azide incorporation on binding affinity by small papain inhibitors 2014 AEM Wammes, TG Hendriks - Bioorganic & medicinal , 2014 - Elsevier ... 20 (b) Docking of leupeptin in the active site of papain (PDB file 1POP). ... 21 Prior to docking we investigated different papain structures of the PDB to explore different ligandpapain complexes, as well as the flexibility of the protein in the area of the binding site. ...
695 3py6 - Influence of CH... O interactions on the structural stability of beta-lactamases 2013 P Lavanya, S Ramaiah, A Anbarasu - Journal of Biological Physics, 2013 - Springer ... We selected a non-redundant data set of 95 ?-lactamases from the Protein Data Bank (PDB) [23] for our ... Table 2 CHEEEO interacting residues in the active site of ?-lactamases PDB ID Active site residues ... 130 Ser 70 Ser 235 Arg 244 Met 69 Tyr 105 Val 216 Gly 236 3PY6-A Arg ...
696 3l56 - Influence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymerase 2011 A Foeglein, EM Loucaides, M Mura? - Journal of General Virology, 2011 - Soc General Microbiol ... The side chains of residues G590 and Q591 are yellow. (c) Surface electrostatic potential modelling (using Swiss-Prot: red indicates negative charge, blue positive charge) on the 627 domain of PR8 or tPB2 (adapted from PDB 3L56; Yamada et al., 2010). ...
697 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
698 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
699 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 ...
700 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
701 3tv2 - Inside Cover: CONFECT: Conformations from an Expert Collection of Torsion Patterns (ChemMedChem 10/2013) 2013 C Sch?rfer, T Schulz-Gasch, J Hert? - ?, 2013 - Wiley Online Library ... frequency histograms (top left). One of the bioactive conformations of AMP is shown in the binding site of the protein from PDB complex 3TV2 (bottom right). For more details, see the Full Paper by Matthias Rarey et al. on p. 1690 ff. ...
702 3k2h - Inside the biochemical pathways of thymidylate synthase perturbed by anticancer drugs: Novel strategies to overcome cancer chemoresistance 2015 L Taddia, D D'Arca, S Ferrari, C Marraccini - Drug Resistance , 2015 - Elsevier The binding sites of other folate analogs (such as methotrexate) have been studied with TS isolated from other organisms (PDB IDs: 3K2H, 1AXW) and all share the same binding site..
703 3r20 - Insight from the structural molecular model of cytidylate kinase from Mycobacterium tuberculosis 2013 NK Verma, B Singh - Bioinformation, 2013 - ncbi.nlm.nih.gov ... known structure (template) of Mycobacterium smegmatis (PDB ID: 3R20) was chosen from proteindatabank (PDB) by using ... experimental structure of cytidylate kinase of Mycobacterium tuberculosis is not yet available in PDB (Protein Data Bank), comparative modeling ...
704 3iml - Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits 2013 N SHAFQAT, JRC MUNIZ, ES PILKA? - Biochem. J, 2013 - 31.24.0.66 ... sequences include hMAT1A (PDB code 2OBV; Uniprot ID Q00266), hMAT2A (PDB code 2P02; Uniprot ID P31153), rMAT1A (PDB code 1O9T; Uniprot ID P13444), eMAT (PDB code 1RG; Uniprot ID P0A817) and Burkholderia pseudomallei MAT (PDB code 3IML; Uniprot ID ...
705 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
706 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
707 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
708 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).
709 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
710 3cez 3cxk, 3eoo Insights into function, catalytic mechanism, and fold evolution of selenoprotein methionine sulfoxide reductase B1 through structural analysis 2010 FL Aachmann, LS Sal, HY Kim, SM Marino? - Journal of Biological Chemistry, 2010 - ASBMB ... Relative to MsrB1, the crystal structures of MsrBs from N. gonorhoeae (PDB code 1L1D) (8), X. campestris (PDB code 3HCI) (36), B. pseudomallei (PDB code 3CEZ/3CXK), S. pneumoniae (PDB code 3E0M) (31), and B. subtilis (3E0O) (31), as well as the solution structure of B ...
711 2ke0 2l2s, 3k2c, 2ko7 Insights into immunophilin structure and function 2011 C Lucke, M Weiwad - Current medicinal chemistry, 2011 - ingentaconnect.com ... 18, No. 35 L?cke and Weiwad Table 1. List of FKBP Structure Coordinates Available in the RCSB Database name organism UniProtKB residues mutation(s) PDB ID method resolution ligand(s) reference ... FKBP burkholderia pseudomallei Q63J95 1-113 2KE0 NMR SSGCIDa ...
712 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
713 4fkx - Insights into mechanism kinematics for protein motion simulation 2014 M Diez, V Petuya, LA Martnez-Cruz - BMC , 2014 - biomedcentral.com ... obtained results have been compared with each proteins' structural data, available on the ProteinData Bank (PDB). The results are shown on Table 2. ... mass (Da) in secondary structures secondary structures (PDB) -helix -sheet -helix -sheet ... 4fkx 55.13 34.8 19.7 42 16 ...
714 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
715 3u40 - Insights into Phosphate Cooperativity and Influence of Substrate Modifications on Binding and Catalysis of Hexameric Purine Nucleoside Phosphorylases 2012 PO de Giuseppe, NH Martins, AN Meza? - PloS one, 2012 - dx.plos.org ... Structural superposition of BsPNP233-Ado (magenta carbon atoms), B. cereus adenosine phosphorylase (BcAdoP)-Ado-SO 4 (green carbon atoms, PDB code 3UAW [52]) and Entamoeba histolytica PNP-Ado (cyan carbon atoms, PDB code 3U40 [55]) complexes. ...
716 3hhj - Insights into substrate recognition by the< i> Escherichia coli</i> Orf135 protein through its solution structure 2012 K Kawasaki, T Kanaba, M Yoneyama? - Biochemical and Biophysical Research Communications, 2012 - Elsevier ... Finally, this study should contribute towards a further understanding of the substrate specificity of Nudix enzymes. For example, the DALI server showed the highest similarity score of 18.9 to the recently published Nudix enzyme (PDB:3hhj) [27]. ...
717 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 ...
718 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
719 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
720 3r1i - Insilico Characterization and Homology Modeling of Arabitol Dehydrogenase (ArDH) from Candida albican 2013 MW Sarwar, IB Saleem, A Ali, F Abbas - Bioinformation, 2013 - ncbi.nlm.nih.gov … used for multiple sequence alignment of ArDH with other dehydrogenases from Mycobacterium marinum (PDB Id: 3R1I), Candida parapsilosis ...
721 3quv - INSILICO CHARACTERIZATION OF TRANSFER RNA (M G37) METHYLTRANSFERASE IN BACTERIA, ARCHAEA AND EUKARYOTA 2011 T Srinivasan, D Sudarsanam - jbstonline.com ... TrmD, aTrm5 and eTrm5 protein was modeled based on the 3QUV-B, 2ZZN-A, and PYX1Ain respectively. ... eTrm5 three dimensional structure is not available in PDB that has distinctlystructural topology to bacterial TrmD. 4. DISCUSSION ...
722 3emk 3ftp, 3f9i, 3enn, 3grp In silico docking of herbal based 'epigallocatechin'onto homology modeled ketoacyl-ACP reductase domain of FAS protein from Mycobacterium tuberculosis H37Rv 2012 KV Ramesh, S Chandy, D Pai? - Indian Journal of Biotechnology, 2012 - nopr.niscair.res.in ... A survey of M. tuberculosis structural genomics consortium25 suggests that the 3D structures of proteins for several regions of M. tuberculosis genome are available in PDB databank, except FAS of H37Rv strain26 ... pdb|3EMK|A Chain A, 2.5a Crystal Structure Of GlucoseRIBITOL ...
723 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
724 3hhe - In silico identification of inhibitors of ribose 5-phosphate isomerase from Trypanosoma cruzi using ligand and structure based approaches 2017 V de VC Sinatti, LPR Baptista, M Alves-Ferreira - Journal of Molecular , 2017 - Elsevier ... Abbreviations: LB, Ligand-Based pharmacophore hypothesis; SB, Structure -Based pharmacophore hypothesis. ... bound to R5P substrate ( PDB ID: 3K7S) and bound to the 4PEH ( PDB ID: 3K8C) [12 ... as query and the 1XTZ (identity of 46%), 1LK7 (identity of 42%), 3HHE (identity ...
725 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
726 3ej0 3gqt In silico modeling of cooperative ligand binding 2011 M Vass - theop11.chem.elte.hu ... binding conformations of ligands. A set of 115 X-ray crystal structures was collected from the RCSB Protein Data Bank (PDB) containing at least two non-cofactor type ligands in close proximity to each other believed to be a result of cooperative binding. The commercial ...
727 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
728 2ke0 - In silico prediction of binding sites on proteins 2010 S Leis, S Schneider, M Zacharias - Current medicinal chemistry, 2010 - ingentaconnect.com ... 15 Leis et al. Table 3. Protein Test Structures pdb entry molecule state ligand Rmsd (?)b 2ANO E.coli dihydrofolate reductase bound Inh. MS-SH08-17 0 ... 1FKS_2VCD 1FKS based on 2VCD structure homology --- 2.3 1FKS_2KE0 1FKS based on 2KE0 structure homology --- 2.6 ...
729 3fs2 - In silico quest for putative drug targets in Helicobacter pylori HPAG1: molecular modeling of candidate enzymes from lipopolysaccharide biosynthesis pathway 2012 M Sarkar, L Maganti, N Ghoshal, C Dutta - Journal of molecular modeling, 2012 - Springer ... Fig. 7 Sequence alignment of 2-dehydro-3-deoxyphosphoocto- nate aldolase of H. pylori HPAG1 with template proteins from Aquifex aeolicus (PDB id: 1fx6), Haemophilus influenza (PDB id: 1o60) and Brucella melitensis (PDB id: 3fs2). ...
730 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
731 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
732 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
733 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
734 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
735 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
736 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
737 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
738 4qfh - Integrao de diferentes abordagens para a avaliao de atividade antiparasitria, propriedades ADMET e alvos celulares de novas Arilimidamidas sobre 2016 CC Santos - 2016 - arca.fiocruz.br OMS Organizao Mundial de Sade PAINS Do ingls Pan-assay Interference compounds PCR Reao em cadeia da polimerase PDB Do ingls Protein Data Bank pKa Constante de ionizao de cidos Pt Pentamidina SdpS Do ingls Spermidine synthase
739 3tcq - Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40 2016 MU Mirza, N Ikram - International Journal of Molecular Sciences, 2016 - mdpi.com ... We have identified VP40 assemblies in a filamentous structure and have shown that disruption of these structures halts viral egress... The homology-based search inferred that the 3D coordinate crystal structure of the Reston Ebola virus RNA binding domain (PDB ID: 3KS4), in addition to the crystal structure of the Sudan Ebola virus matrix protein VP40 (PDB ID: 3TCQ), were the best hits based on query coverage ...
740 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
741 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
742 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
743 3mmt - Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non 2016 CM Carnielli, J Artier, JCF de Oliveira- Data in brief, 2016 - Elsevier ID, Gene symbol, ENSEMBL, SWISS-PROT, Protein structure ( PDB ), Conserved domain (CDD), Gene ontology (GO) GO:0003735 structural constituent of ribosome citri (strain 306) GN=XAC3344 PE=3 SV=1, 3mmt Fructose-bisphosphate aldolase, cd00948, FBP_aldolase_I_a
744 3mmt - Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non- 2016 CM Carnielli, J Artier, JCF de Oliveira - Data in Brief, 2016 - Elsevier ... ID, Gene symbol, ENSEMBL, SWISS-PROT, Protein structure (PDB), Conserved domain (CDD),Gene ontology (GO). ... GO:0003735 structural constituent of ribosome, ... citri (strain 306) GN=XAC3344PE=3 SV=1, 3mmt Fructose-bisphosphate aldolase, cd00948, FBP_aldolase_I_a ...
745 3jst - Interactions with the Bifunctional Interface of the Transcriptional Coactivator DCoH1 Are Kinetically Regulated 2014 D Wang, MW Coco, RB Rose - Journal of Biological Chemistry, 2014 - ASBMB ... The prokaryotic and archaeal PCD are obligate dimers ((19) and pdbid 3jst, 2ebb, 1uso ... with theCCP4 program Phaser (30) using the 1.6 Å wild-type DCoH2 structure (PDB ID: 1RU0 ... asymmetricunit, forming a tetramer with a symmetry-related dimer (1). The structure is identical ...
746 5dvw 3tcq Interplay Among Constitutes of Ebola Virus: Nucleoprotein, Polymerase L, Viral Proteins 2017 M Zhang, P He, J Su, DT Singh, H Su - Biophysical Reviews and , 2017 - World Scientific ... interacts with the C-terminal domain of NP to stabilize the overall virion structure (shown in ... Majorfunctions of these structural proteins are elaborated in the boxes.1,10,56 (b) Crystal ... of Ebola viralproteins: NP (RCSB PDB:4ZTI)96; VP30 protein (RCSB PDB:5DVW)97; VP35 ...
747 4gri 4g6z Interplay between Catalysts and Substrates for Activity of Class Ib Aminoacyl-tRNA Synthetases and Implications for Pharmacology 2016 P Stephen, SX Lin, R Gieg - Current topics in medicinal , 2016 - ingentaconnect.com ... Eukarya) and limited records for ArgRS (13 PDB entries) and LysRS-1 (1 PDB entry ... with that ofEcoGlnRS and dem- onstrated the presence of GluRS-specific secondary-structure insertions ...aaRS:small ligands Eco (4OBY) Bbu(4GRI) Bth(4G6Z) Tel (2CFO) Tma (3AFH) Tth (1J09 ...
748 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
749 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
750 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
751 3gvh - Investigating Bias in Protein Properties Inferred via Ancestral Sequence Reconstruction 2017 A Rickett - 2017 - scholarsbank.uoregon.edu We formulate and analyze the electrostatics of 14 distinct protein families, each containing PDB structures of structural elements, send signals from cell to cell, and much more. Every protein sequence defines a unique 3-dimensional structure which a protein assumes through a
752 2khr 2kvc Investigating conformational transitions of proteins by coarse-grained elastic network models 2012 M Tekpinar - 2012 - search.proquest.com The model is the green tube representation and the target ( PDB ID: 1LST) is the dark blue tube. Residues 91 B- factors show that each atom in the structure is dynamic in side chains of their amino acids. However, some conformations can have large structural
753 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<
754 3u04 - Investigating the Antiproliferative Activity of Synthetic Troponoids 2016 ER Falcone - 2016 - digitalcommons.uconn.edu ... 1.21 Crystal structure (PDB: 3u04) of Actinonin (green) bound to PDF of Ehrlichia chaffeensis(cyan ... 1.36 Crystal structure (PDB: 2y9x) of tropolone (green) bound to tyrosinase from Agaricusbisporus (cyan ... 2.2 Structures of some natural tropolones that exhibit antimicrobial activity ...
755 4giv - Investigating the molecular architecture of yeast histone acetyltransferase complexes 2016 D Setiaputra - 2016 - open.library.ubc.ca Learning, knowledge, research, insight: welcome to the world of UBC Library, the second-largest academic research library in Canada.
756 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 ...
757 4dq8 3r9p, 3p4i, 4ijn Investigation of pyrophosphate versus ATP substrate selection in the Entamoeba histolytica acetate kinase 2017 T Dang, C Ingram-Smith- Scientific Reports, 2017 - ncbi.nlm.nih.gov ... ID 3P4I; Mycobacterium paratuberculosis, PDB ID 3R9P; Mycobacterium marinum PDB ID 4DQ8 . ... ACK structures were downloaded from Protein Data Bank ( PDB ): 4H0O (Entamoeba ... Structure superposition and modeling were performed using Accelrys Discovery Studio 3.5 ...
758 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
759 4ohc - Investigations into patterns of interactions involving sequentially neighboring amino acids in functional proteins 2016 M Sule - 2016 - dspace.ncl.res.in Figure 6. The alpha helix in PDB : 3KB9 with the side chain hydrogen bonding pattern between While most motifs comprise primarily of regular secondary structures such as -helices or -sheets, the regions connecting these structural elements are irregular structure elements
760 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
761 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
762 3h7f - In vivo protein tyrosine nitration in Arabidopsis thaliana 2011 J Lozano-Juste, R Colom-Moreno? - Journal of experimental botany, 2011 - Soc Experiment Biol ... protein models were generated by homology modelling at the SWISS-MODEL workspace (Arnold et al., 2006) using the coordinates of GAPDH from rat (PDB code 2VYN), serine hydroxymethyltransferase from Mycobacterium tuberculosis (PDB code 3H7F), transketolase ...
763 3u03 - Iron depletion strategy for targeted cancer therapy: utilizing the dual roles of neutrophil gelatinase-associated lipocalin protein 2016 HC Tang, PC Chang, YC Chen - Journal of molecular modeling, 2016 - Springer ... and 3D crystal conformation of human NGAL protein was acquired from Protein Data Bank (PDBID: 3U03). The ligand inside 3U03 was removed. ... We illustrated root mean square fluctuation(RMSF), database of secondary structure assignment and component (DSSP), smallest ...
764 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
765 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
766 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
767 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
768 3ek2 3k2e, 3grk < i> Staphylococcus aureus</i> FabI: Inhibition, Substrate Recognition, and Potential Implications for In Vivo Essentiality 2012 J Schiebel, A Chang, H Lu, MV Baxter, PJ Tonge? - Structure, 2012 - Elsevier ... bacteria harbor an alanine at this position and, thus, lack the required hydrogen bond acceptor (Figure 3). Consistently, all structurally characterized FabIs from gram-negative organisms contain just a single flexible SBL (PDB codes 2JJY, 2P91, 2WYU, 3EK2, 3GRK, and 3K2E ...
769 3fvb - I. Synthesis Of Anthraquinone Derivatives For Electron Transfer Studies In DNA. II. Characterization Of The Interaction Between Heme And Proteins. 2011 Y Cao - 2011 - scholarworks.gsu.edu ... 64 Figure 3.2 (A) The active site of HSA (PDB ID 1N5U); Lys190 is in blue; (B) The active site of Mb (1WLA); Lys45 and Lys96 are in blue. ... (A) The IsdA (PDB ID: 2ITF) binding pocket; (B) the IsdC (PDB ID: 2O6P) binding pocket; (C) the Shp (PDB ID: 2Q7A) ...
770 5eqz - Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization 2017 A Ouali, D Allouche, S De Givry- on Uncertainty in, 2017 - hal.archives-ouvertes.fr Variable Neighborhood Search (VNS) (Mladenovic and Hansen, 1997) is a metaheuristic that uses a finite set of pre-selected neighborhood structures Nk,k = 1, 2, ..., kmax to escape from local minima by system- atically changing the neighborhood structure if the cur- rent one
771 4fzi - < i> Trypanosoma cruzi</i> chemical proteomics using immobilized benznidazole 2014 A Trochine, G Alvarez, S Corre, P Faral-Tello - Experimental , 2014 - Elsevier ... Murta et al., 2006). In addition, TcOYE and TcAKR have equivalent tertiary structures. TcAKR was crystallized in the apo form and its structure was recently deposited at a 2.6 resolution [PDB: 4fzi]. The protein has an (alpha ...
772 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
773 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
774 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
775 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
776 3k9w - Kinetic, Thermodynamic, and Structural Insight into the Mechanism of Phosphopantetheine Adenylyltransferase from< i> Mycobacterium tuberculosis</i> 2010 TJ Wubben, AD Mesecar - Journal of molecular biology, 2010 - Elsevier ... 21 Enteroccoccus faecalis, 22 and Helicobacter pylori; 23 and Staphylococcus aureus in complex with 3'-phosphoadenosine 5'-phosphosulfate, 24 Burkholderia pseudomallei in complex with hydrolyzed dPCoA [Protein Data Bank (PDB) ID 3K9W; unpublished], and ...
777 3ief 3knu Landscape of Intertwined Associations in Multi-Domain Homo-Oligomeric Proteins 2015 SS MacKinnon, SJ Wodak - Journal of molecular biology, 2015 - Elsevier ... In addition, we identified protein structures in the PDB related to each member of our ... We examineddomain re-orientations in these relatives and how the quaternary structure is affected ... This allowedus to characterize the level of structural plasticity in protein families comprising ...
778 3k2h - Large-scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real 2014 T Krotzky, C Grunwald, U Egerland… - Journal of chemical …, 2014 - ACS Publications ... Again, we searched the PDB for proteins that bind pemetrexed and found six structures: four thymidylate synthases (1JUJ, 1JU6, 3K2H, 4FQS), a folate receptor (4KN2), and a pteridine reductase (2X9G). By culling this set of proteins using PISCES ...
779 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
780 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
781 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
782 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
783 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.
784 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
785 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)
786 3p0x - Lifting the lid on GPCRs: the role of extracellular loops 2012 M Wheatley, D Wootten, MT Conner… - British journal of …, 2012 - Wiley Online Library ... Family A GPCRs: ECL structural aspects. ... 2RH1); B, D3R (yellow; PDB accession 3PBL); C, A2A R (orange; PDB accession 2YDO); D, CXCR4 (green; PDB accession 3OE0). ... In contrast, theECL2 of the β 2 AR possess a radically different structure comprising a short α-helix that ...
787 4qfh - Ligand docking and binding site analysis with pymol and autodock/vina 2015 MA Rauf, S Zubair, A Azhar - International Journal of Basic and …, 2015 - sciencepubco.com ... In recent years, the process of virtual screening technique for docking small molecules into aknown protein structure is a powerful tool for drug ... Enter the name of Protein or enzyme that willbe used for docking studies (For example, Glucose 6 Phosphate or its pdb id 4QFH). ...
788 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
789 4eqy - Lipid A Biosynthesis of Multidrug-Resistant Pathogens-A Novel Drug Target 2013 CR Lee, J Hun Lee, B Chul Jeong? - Current pharmaceutical design, 2013 - ingentaconnect.com ... (B) Structure of Burkholderia thai- landensis LpxC homotrimer (PDB ID, 4EQY). This structure shows that the catalytic residue (red) and the substrate-binding residues (blue) clustered around the hydrophobic cleft located between adjacent monomers. ...
790 3qh4 - Lipid Inclusions in Mycobacterial Infections 2013 M Stehr, AA Elamin, M Singh - 2013 - intechopen.com ... Furthermore the three-dimensional structures of the esterases Rv0045c (PDB 3P2M) [78], Rv1847 (PDB 3S4K), and LipW (3QH4) from M. tuberculosis have been determined, but unfortunately it is not known whether these enzymes are involved in TAG hydrolysis. 3.5. ...
791 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...
792 3qi6 3ndn, 3qhx l-Methionine Production 2016 J Shim, Y Shin, I Lee, SY Kim - 2016 - Springer ... 1CS1 [73]) was aligned to MetB of Mycobacterium ulcerans (PDB ID: 3QI6, 3QHX [74 ... jejuni (PDBID:4OC9 [75]), and MetZ of Mycobacterium tuberculosis (PDB ID: 3NDN ... substrate specificity inthese four enzymes is required to establish detailed structurefunction relationships. ...
793 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
794 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
795 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
796 3uam - Lytic polysaccharide monooxygenases: a crystallographer's view on a new class of biomass-degrading enzymes 2016 KEH Frandsen, L Lo Leggio - IUCrJ, 2016 - scripts.iucr.org ... addi- tional evidence of the synergy between GH61 and cellulose- degrading glycoside hydrolaseswas presented, together with structure-based mutagenesis ... In the case of LPMOs structuralknowledge really can claim to have driven functional understanding. ... PDB code ASU ...
797 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
798 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
799 3p96 3km3, 3k9g Macromolecular X-ray structure determination using weak, single-wavelength anomalous data 2014 G Bunkóczi, AJ McCoy, N Echols… - Nature …, 2014 - nature.com ... phasing, accounting for 73% of such structures deposited in the Protein Data Bank (PDB;http://www.pdb.org/) 1 in 2013. In the SAD method, the X-ray diffraction from anomalouslyscattering atoms in a molecule provides X-ray phase information for the entire crystal structure ...
800 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
801 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
802 3eoo - Massenspektrometrische Untersuchungen zur Struktur der Peroxisom-Proliferator-aktivierten Rezeptoren- und-/ 2017 R Schwarz - 2017 - opendata.uni-halle.de Optische Dichte bei 600 nm PAGE Polyacrylamid-Gelelektrophorese PBP PPAR Binding Protein PCR Polymerase-Kettenreaktion PDB Proteindatenbank PflB Pyruvate Formate Lyase PMSF Phenylmethansulfonylfluorid PPAR Peroxisom-Proliferator-aktiverter Rezeptor ppm ... Die umfangreichsten Röntgenkristallstrukturen wurden mit dem Subtyp PPAR-γ (PDBEinträge: 3DZU, 3DZY und 3EOO) gewonnen, in denen das Volllängenprotein ohne den flexiblen N-Terminus mit RXR-α und verschiedenen Liganden und Kofaktoren kokristallisier
803 3p32 - Mathematical Modeling and Screening of Ligand Binding Sites in Protein using the Tetrahedral Motif Method and Double-Centroid Representation 2012 VM Reyes - 2012 - ritdml.rit.edu ... unannotated structures in PDB with unknown function to identify possible candidates that might have FMN bound to them. _ + ... Structures from the PDB for Screening using the screening procedure established for the above mathematical model for the binding site.[11] Page 19. ...
804 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
805 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
806 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
807 3ezn - Mechanism of Dephosphorylation of Glucosyl-3-phosphoglycerate by a Histidine Phosphatase 2014 Q Zheng, D Jiang, W Zhang, Q Zhang, Q Zhao - Journal of Biological Chemistry, 2014 - ASBMB ... 2B). Other significant structural matches included phosphoserine phosphatase 1 (34) (PsP1; Protein Data Bank code 4IJ5) and phosphoglycerate mutase (35) (PGM; Protein Data Bank code 3EZN). ... PDB, Protein Data Bank. ...
808 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
809 4kna - Mechanisms of recognition of A monomer, oligomer, and fibril by homologous antibodies 2017 J Zhao, R Nussinov, B Ma- Journal of Biological Chemistry, 2017 - ASBMB ... To get structural insight into A recognition by crenezumab, we compare the ... Two possible conformers of the apo form of the crenezumab Fab structure were modeled based on the crystal structures of CreneFab apo ( pdb code: 5kmv) and CreneFab-A ( pdb code: 5kna ...
810 3ftp 4lfy Mechanistic and Functional Characterization of Lactonases of COG3618 in the Amidohydrolase Superfamily 2014 ME Hobbs - 2014 - oaktrust.library.tamu.edu ... -strands. Twenty years later, we have a deeper understanding of the structural, catalytic, andmechanistic diversity of this superfamily. ... octahedral geometry (Figure 1.1B). In the crystal structureof the Mn/Mn PTE the alpha Page 18. 6 ... (A) White (pdb code 1hzy) and light blue ...
811 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
812 4iz9 - Mechanistic features of< i> Salmonella typhimurium</i> propionate kinase (TdcD): Insights from kinetic and crystallographic studies 2013 S Chittori, DK Simanshu, S Banerjee? - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2013 - Elsevier ... The recently deposited structure of Mycobacterium avium acetate kinase (PDB ID: 4IZ9; unpublished results) determined in complex with succinic acid–APC (a nucleotide analog) conjugate also shows a bound EDO at the proposed SCFA-II site ( Supplementary Fig. S1) consistent with the conserved nature of ligand binding mechanism in acetokinase family of enzymes ...
813 3tmg - Mechanistic insight into trimethylamine N-oxide recognition by the marine bacterium Ruegeria pomeroyi DSS-3 2015 CY Li, XL Chen, X Shao, TD Wei, P Wang - Journal of , 2015 - Am Soc Microbiol ... The extended loop comprising the metal ion binding site is colored orange. The PDBcode of each structure is shown. ... TmoX, green; 2REG, cyan; 3TMG, magenta; 3L6H, yellow;1R9L, salmon; 3PPP, light blue; 3R6U, slate; 1SW2, orange. ...
814 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
815 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
816 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
817 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
818 3sdw - Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of Streptococcal isomerase and … 2015 Y Maruyama, S Oiki, R Takase, B Mikami… - Journal of Biological …, 2015 - ASBMB ... Owing to the high sequence identity, the overall structure of SagDhuI was highly similar to threegroup I-protein structures from S. pneumoniae (PDB code 2PPW), Novosphingobium ... In contrast,group II proteins (PDB codes 1NN4, 3K8C, 3HEE, and 3SDW), which consist of ...
819 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
820 3fdz - Metabolic Signaling and Therapy of Lung Cancer 2013 J Chen - 2013 - DTIC Document ... PGAM1. (A) Cartoon representation of 2,3- BPG location from structure 3FDZ superposed on PGAM1 (PDB ID: 1YFK). H11 and Y92 are directly proximal to and Y26 is also close to cofactor (2,3-BPG)/substrate (3-PG) binding site. ...
821 3r0o - Metabolism of β-valine via a CoA-dependent ammonia lyase pathway 2015 M Otzen, CG Crismaru, CP Postema, HJ Wijma… - Applied microbiology …, 2015 - Springer ... to the Thermus thermophilus PaaG (35 % identity), a predicted 2, 3-dehydroadipyl-CoA hydrataseof which the structure is solved (PDB 3HRX ... searches of the protein encoded by ORF12 showedhomology to Mycobacterium avium carnitinyl-CoA hydratase (3R0O; 48 % identity ...
822 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
823 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,
824 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
825 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
826 3mx6 - Methionine aminopeptidase as a target for the discovery of novel antibacterial agents 2016 C Chen - 2016 - search.proquest.com ... 14. Figure 2-1. Crystal structure of RpMetAP I (PDB ID: 3MX6, Edwards T. et. al., 2010). Metalions shown in the active site as spheres are two Mn (II) ions. 15. Materials and Methods.Screening of suitable induction conditions for expression of RpMetAp I. ...
827 3cez 3cxk Methionine sulfoxide reductase B displays a high level of flexibility 2009 FM Ranaivoson, F Neiers, B Kauffmann? - Journal of molecular Biology, 2009 - Elsevier ... View thumbnail images View high quality image (983K). Two X-ray structures of MsrB from Neisseria gonorrhoeae [Protein Data Bank (PDB) ID 1L1D 12 ] and Burkhodelia pseudomallei (PDB IDs 3CXK and 3CEZ; unpublished results) have been determined so far. ...
828 3cxk - Methionine sulfoxide reduction in ciliates: Characterization of the ready-to-use methionine sulfoxide-< i> R</i>-reductase genes in< i> Euplotes</i> 2013 N Dobri, EEN Oumarou, C Alimenti, C Ortenzi? - Gene, 2012 - Elsevier ... The crystallographic structure of the Burkholderia pseudomallei MsrB (PDB ID: 3cxk) was automatically selected by the server as a template since it shows an amino acid sequence identity of 53% and 56% with the MsrB protein of E. raikovi and E. nobilii, respectively. ...
829 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
830 4efi - Methods for the site-selective introduction of halogen into natural products 2016 MCY Chang, MC Walker, BW Thuronyi- US Patent App. 14/913,601, 2016 - Google Patents domain. The NphT7 structure was predicted using Phyre2 (Kelley, et al., Nat. Prot., 4:363-371 (2009)) and based on a type III 3-oxoacyl-(acyl-carrier protein) synthase from Burkholderia xenovorans ( PDB ID 4EFI ). Despite
831 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
832 3krb - Methylglyoxal metabolism in Leishmania infantum 2010 LIS Barata - 2010 - repositorio.ul.pt ...Besides the human enzyme, there are also accessible other aldose reductase structures from other organisms, including the protozoan Giardia lamblia (PDB entry 3KRB (Seattle Structural Genomics Center for Infectious Disease, to be published)) and the mammal Sus scrofa (PDB entry 1AH4 (Urzhumtsev et al. 1997)).. ...
833 2kn9 - Metodos Computacionais para o Calculo de Estruturas de Proteinas: Aproximando o Problema Molecular de Geometria de Distancias de Dados de Ressonancia Magnetica Nuclear 2010 PC Nucci - ic.uff.br ... PMGD Problema Molecular de Geometria de Dist?ncias PMGDD Problema Molecular de Geometria de Dist?ncias Discreto BP Branch-And-Prune RMN Resson?ncia Magn?tica NuclearPDB Protein Data Bank pH Potencial Hidrogeni?nico 12 Page 14. Cap??tulo 1 Introdu??ao ...
834 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
835 4h51 - Mitochondrial selfish elements and the evolution of biological novelties 2016 L Milani, F Ghiselli, M Passamonti - Current Zoology, 2016 - cz.oxfordjournals.org ... and to better show the structure of both male and female acinus (ie, the structural unit of ... The tertiarystructure of RPHM21 and RPHF22 was predicted using I-TASSER (http://zhanglab.ccmb.med ...The best model in pdb format was used as input for the Chimera 1.8.1 software ...
836 3oc6 - Mn2+ and Mg2+ synergistically enhanced lactic acid production by Lactobacillus rhamnosus FTDC 8313 via affecting different stages of the hexose monophosphate pathway 2014 LC Lew, SB Choi, PL Tan? - Journal of applied microbiology, 2013 - Wiley Online Library ... No. Enzyme, PDB ID, FEB (kcal mol ?1 ). Without ion, Mg 2+, Mn 2+, Mg 2+ and Mn 2+. PDB, Protein Data Bank. a ... 2, Glucose-6-phosphate dehydrogenase, 1DPG, ?4E79, ?4E74, ?4E52, ?8E59a. 3, 6-phosphogluconolactonase, 3OC6, ?6E98, ?6E66, ?6E58, ?7E09. ...
837 3oa1 - Modelado del Monómero de la Fosfoproteína del Virus de la Rabia 2015 EMD González, FGB González, JC Basurto… - smbb.com.mx ... PDB ID Description 1VY1 Dominio del C-Terminal de la polimerasa del virus de la rabia 3OA1Cristal de ... IPN – ESM Bibliografía. 1. Ivanov , I., Crépin, T., Jamin, M., & Ruigrok, RH (10 de Enerode 2010). Structure of the Dimeration Domain of the Rabies Virus Phosphoprotein. ...
838 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
839 3q8n - MODELING AND DOCKING STUDIES OF 4-AMINOBUTYRATE AMINOTRANSFERASE FOR HUNTINGTON'S DISEASE. 2011 H Pareek, P Thakur, D Ray - International Journal of Pharma & Bio Sciences, 2011 - search.ebscohost.com ... desired protein ie GABA-AT using a template sequence with PDB code 3Q8N. The constructed 3D models were checked for DOPE score and Ramachandran plot respectively with Modeller 9v8 and PROCHECK. Results are shown in Table 1. Model No. ...
840 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
841 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
842 3dah - Modeling of Protein Flexibility and Inter-Molecular Interactions: Applications to Computer-Aided Drug Design and Discovery 2012 R Ai - 2012 - escholarship.org ... Page 22. xxi Figure 5.1 .95 Summary of ligand binding capacity and subdomains of HSA using PDB structure 1E7E. Long-chain fatty acids are depicted in VDW representation using VMD 1.8.7. ...
843 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
844 3ecd - Model the Solvent-Excluded Surface of 3D Protein Molecular Structures Using Geometric PDE-Based Level-Set Method 2009 Q Pan, XC Tai - Communications in Computational Physics, 2009 - uib.no ... where ? is a very small value and chosen to be O(?x). 3 Numerical implementation 3.1 Initial construction The data of the complex 3D protein molecular structures, saved as pdb format files, can be downloaded from the free website of the protein data bank: http://www.rcsb.org. ...
845 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
846 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