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 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 .... ...
2 3uam - Studies on structures of novel sugar metabolic enzymes 2015 - 2015 - repository.dl.itc.u-tokyo.ac.jp ... Page 10. 4 Table 1-1 Classification of structure-known LPMOs. Organisms Protein Name FamilyPDB Fungi Hypcrea jecorina GH61B AA9 2VTC Thielavia terrestris GH61E AA9 3EII, 3EJA ...Burkholderia pseudomallei CBM33 AA10 3UAM 1-1-2 Enzymes in Leloir pathway ...
3 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). ...
4 3quv - Structural Studies of Csd6 Protein from Helicobacter pylori and Rv2258c Protein from Mycobacterium tuberculosis 2016 - 2016 - s-space.snu.ac.kr ... Figure 2-3. Dimeric structure and the oligomeric state of Rv2258c 112 Figure 2-4. Sequence alignment of Rv2258c with its close structural homologs 117 ... Figure 2-6. Comparison of monomer structures of Rv2258c-SFG and M. ...
5 3o0h - Structure of flavoprotein RclA from food-borne pathogens, and its molecular mechanism contributing to hypochlorous acid resistance 2020 - 2020 - s-space.snu.ac.kr representation is labeled with residue numbers of three proteins (first RclA, second 3O0H , third 4M52). Page 36. 26 3.4 I searched for the closest protein to RclA in terms of structure using the DALI server (30). Mercuric reductase (MerA) ( PDB code: 4K7Z), a group II FDR
6 4dgq - Structural and Biophysical Characterization of human NDRG3, a key component of lactate-induced hypoxia responses 2020 - 2020 - s-space.snu.ac.kr 85 Figure 49 Structural comparison of C rmsd values at 5 mM and 87 Figure 51 Molecular dynamic simulation on NDRG3 C30S structure for 100 picoseconds PCR Polymerase chain reaction PDB Protein data bank PEG Polyethylene glycol
7 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. ...
8 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,
9 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
10 6cfp - New anti-viral drugs for the treatment of COVID-19 instead of favipiravir 2020 A Akta, B Tzn, R Aslan, K Sayin- Biomolecular Structure, 2020 - Taylor & Francis According to Table 2, the 6CFP protein is not inhibited by any ligands RNA polymerase proteins with PDB IDs of 6NUR and 6NUS were reported in late 2019 and early In this calculation, the ligand and protein are flexible and solvent molecules surround the entire structure
11 6mfk - Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species 2019 A Alcala, G Ramirez, A Solis, Y Kim, K Tan- Protein, 2019 - Wiley Online Library from P. aeruginosa ( PDB IDs: 1XAT, 2XAT7) and E. anophelis ( PDB ID: 6MFK ). Known SAT 1(A)]. When we compared our structures of the Vibrio proteins with CATs and SATs from the PDB , we found the The AfCAT structure had
12 3s6d - Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei 2016 AA Lopez-Zavala, JS Carrasco-Miranda - et Biophysica Acta (BBA , 2016 - Elsevier ... Glycolysis is one of the most regulated metabolic pathways, however little is known about thestructural mechanisms for its regulation in non-model ... Using the DALI server [53] to look for similar structures, the root mean square deviation (RMSD) for backbone carbons between LvTIM and...P. falciparum (1WOB) 1.5 A, Coccidioides immitis (3S6D) 2.1 A
13 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) ...
14 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
15 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.
16 3hwi - Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle 2012 A Bagchi - Molecular Biology Reports, 2012 - Springer ... like protein) from Mycobacterium tuberculosis (PDB code: 3HWI) with sequence identity of 34 %. ... The predicted structure is similar to the crystal structure of probable thiosulfate sulfurtransferase Cysa2 (rhodanese-like protein) from Mycobacterium tuberculosis (PDB code: 3HWI). ...
17 5eo6 4exq, 4wsh Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product 2017 A Bailey, R Webster, R Hunter, N Freemantle, G Rait - 2017 - Microbiol Mol Biol Rev The crystal structure of the P. aeruginosa enzyme shows that it is composed of Interestingly, crystal structures of P. aeruginosa variants with cysteine substitutions show decreasing Although structural information on porphobilinogen synthases from many sources shows that the
18 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...
19 3p32 - Prediction of Flavin Mononucleotide (FMN) Binding Sites in Proteins Using the 3D Search Motif Method and Double-Centroid Reduced Representation of Protein 3D Structures 2015 A Banerjee, VM Reyes - arXiv preprint arXiv:1602.08119, 2015 - arxiv.org ... Since this work utilizes the benefits of using a DCRR structure as opposed to a AAR structureas discussed above one of the very important steps is to convert the structures into DCRR onesfrom the default AAR structure given in PDB. There can be two ways of doing this. ...
20 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
21 6nb6 6nb7 Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2 2020 A Basu, A Sarkar, U Maulik- Scientific reports, 2020 - nature.com Every coronavirus comprises four structural proteins namely spike, envelope, nucleocapsid and membrane proteins Similarly, PDB ID 6M17 shows the presence of sodium-dependent neutral amino acid transporter B(O)AT1 in its structure
22 6wsa 4ghk, 4rgb, 3sgw, 4w5k, 3kcq, 3oxk, 3ppi Principal component analysis of alpha-helix deformations in transmembrane proteins 2021 A Bevacqua, S Bakshi, Y Xia- PloS one, 2021 - journals.plos.org 6tt4, 6txw, 6tzj, 6uqw, 6v47, 6vbj, 6vie, 6vjd, 6vmz, 6vnw, 6w1w, 6w2x, 6wok, 6wsa , 6x1q, 6x2m and the contribution of each physical deformation to the overall flexibility of the secondary structure N -helices of a given length (L residues) were collected from PDB entries (See
23 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
24 3nrr - Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities 2016 A Bhosle, N Chandra - FEBS Journal, 2016 - Wiley Online Library ... due to conservation of overall structure makes it feasible to study variation at each ... C9 (P.falciparum:Tyr 57 and Phe 223; PDB ID: 1J3I), B.bovis (Phe 40 and Phe 161; PDB ID: 3NRR), C.hominis(Phe 35 and Phe 172; PDB ID: 3HJ3) and E.faecalis (Phe 30 and Tyr ...
25 5ucm - trans-Editing by aminoacyl-tRNA synthetase-like editing domains 2020 ABK Nagy, M Bakhtina- Biology of Aminoacyl, 2020 - books.google.com bound by an autonomous trans- editing factor, such as C. crescentus ProXp-ala ( PDB ID: 5VXB PheRS is also unique in its oligomeric structure it is a heterote- tramer domain ( bound in an editing active conformation will be needed to fully understand the structural basis for
26 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 ...
27 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 ...
28 4f47 - Post-translational Succinylation of Mycobacterium tuberculosis Enoyl-CoA Hydratase EchA19 Slows Catalytic Hydration of Cholesterol Catabolite 3-Oxo-chol-4,22 2020 AC Bonds, T Yuan, JM Werman, J Jang- ACS Infectious, 2020 - ACS Publications Cholesterol is a major carbon source for Mycobacterium tuberculosis (Mtb) during infection, and cholesterol utilization plays a significant role in persistence and virulence within host macrophages...
29 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), ...
30 6axe 4ex4 The glyoxylate shunt as a target for antibacterial intervention in Pseudomonas aeruginosa 2019 AC McVey - 2019 - aspace.repository.cam.ac.uk The structure of MSG from four prokaryotic species has been resolved by X-ray crystallography: E. coli... Mycobacterium marinum (PDB entry 6AXE), and Mycobacterium leprae (PDB entry 4EX4). Also, the E. coli MSG structure has been solved by NMR
31 4ex4 - Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa 2017 AC McVey, P Medarametla, X Chee, S Bartlett- Biochemistry, 2017 - ACS Publications ... G. Inactivation of these enzymes has been reported to abolish the ability of P. aeruginosa to establish infection in a mammalian model system, yet we still lack the structural information to support drug design efforts. In this work, we describe the first X-ray crystal structure of P ...
32 6wpt - The SARS-CoV-2 spike glycoprotein as a drug and vaccine target: Structural insights into its complexes with ACE2 and antibodies 2020 AC Papageorgiou, I Mohsin- Cells, 2020 - mdpi.com 3. S protein Structural Details The reported structure revealed an asymmetric trimer and two conformations for one of the RBDs: up and down (Figure 3). The ACE2 binding was recently investigated in more detail, resulting in ten structures with the RBDs at different stages of ... Cryo-Electron Microscopy (Cryo-EM) structure of S309 antibody with the S glycoprotein trimer (PDB id 6wpt). The antibody chains are colored in cyan (L chain) and cornflower blue (H chain)
33 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
34 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
35 6mb1 6maz, 6may, 6mb0 N-myristoyltransferase inhibitor binding mode and phenotype in the malarial parasite. 2019 AC Schlott - 2019 - spiral.imperial.ac.uk lacks myristoylation and instead contains a hydro- phobic N-terminal sequence interacting with the Golgi membrane; its location resembles the distribution of GRASP1, but its structure may result 2010) N-Myristoyltransferase from Leishmania donovani: Structural and Functional ... One of them is the aminomethylindazole series including compounds IMP-0917 (PDB: 5O6H) (Mousnier et al. 2018), and IMP-1002 (PDB: 6MB1) (Schlott et al. 2019)
36 4wny - Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications 2018 AC Vollmer, SJ Bark- Advances in applied microbiology, 2018 - Elsevier Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified t... Universal stress protein 4WNY B. pseudomallei Abendroth, Dranow, Lorimer, and Edwards (2008)
37 3mpd 3ndo, 3r8c, 3ngf, 3tcr, 3s4k, 3te8, 3r1j, 3qiv, 3sp1, 3qat, 3tcv, 3pm6, 3tsm, 4dhk, 4dyw, 4eg0, 3urr, 4i1u, 4f4f, 4je1, 4f3y, 4f82, 4lw8, 4pq9, 4q6u, 4ony, 4ose, 4kyx, 4o3v, 4pfz, 4qji, 4oo0, 4q14, 4oh7, 4wso, 3ol3 Statistical Potentials for Prediction of Protein-Protein Interactions 2015 A Dhawanjewar - 2015 - 210.212.192.152 ... protein complexes by reducing the kinetic costs associated with structural rearrangements atthe protein 3 Page 13. Introduction binding sites (Rajamani et al., 2004). ... structure. Around 89 %of structures in the PDB are determined using X-ray Crystallography. How- ...
38 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
39 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
40 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
41 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 (
42 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 ...
43 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. ...
44 3cez - Order and disorder in proteins 2011 A Ertekin - 2011 - mss3.libraries.rutgers.edu ... 83 Figure 4.8 The superimposition of 2.6 ? X-ray crystal structure (PDB ID: 3E0O) and sparse-constraint NMR structures for MsrB from B. subtilis. ... NOESY: Nuclear Overhauser Effect Spectroscopy PDB: Protein data bank PSI: Protein Structure Initiative ...
45 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...
46 6xdh - SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets 2021 AF Alsulami, SE Thomas, AR Jamasb- Briefings in, 2021 - academic.oup.com release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures , our group ... (v) Nsp15 (Uridylate specific endoribonuclease)—PDB Id: 6XDH.
47 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 ...
48 6vxx - Structural impact of mutation D614G in SARS-CoV-2 spike protein: enhanced infectivity and therapeutic opportunity 2020 A Fernndez- ACS medicinal chemistry letters, 2020 - ACS Publications Figure 1. Structural and epistructural interactions at the S1/S2 interface in the spike protein of SARS-CoV-2. (a) Positioning of D614 in the S1 chain (magenta) relative to T859 in the S2 chain (blue) at the S1/S2 interface for the spike protein structure reported in PDB6VXX
49 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.. ...
50 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. ...
51 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). ...
52 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 ...
53 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
54 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). ...
55 4o5h - Structure and biochemistry of phenylacetaldehyde dehydrogenase from the Pseudomonas putida S12 styrene catabolic pathway 2017 AG Crabo, B Singh, T Nguyen, S Emami - Archives of Biochemistry , 2017 - Elsevier ... The closest structural homolog to NPADH is sheep liver aldehyde dehydrogenase ALDH1 (PDBID: 1BXS), which catalyzes the conversion of retinal to retinoic ... In a homologous PADH structure from Burkholderia cenocepacia J2315 (BcPADH) (PDB ID: 4O5H), which was recently solved by the Seattle Structural Genomics Consortium and has 49% identity and 65% similarity to PADH, this loop contains the same number of amino acids as NPADH and adopts a different orientation (Fig. 2C)...
56 3k5p - Molecular modeling of human neutral sphingomyelinase provides insight into its molecular interactions 2011 AG Dinesh, PS Suresh, C Thirunavukkarasu - , 2011 - 033ce13.netsolhost.com ... Based on these results, WD repeat-containing protein 5 from Escherichia coli (PDB code: 3EMH)was selected as a ... Furthermore, we have predicted the structure of a ternary complex whichprovides a better understanding of the molecular interactions ... Pcons5 1ZWX 3K5P 3L1W ...
57 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
58 3k9w - Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii 2019 A Gupta, PK Singh, N Iqbal, P Sharma- et Biophysica Acta (BBA, 2019 - Elsevier PDB ID: 3ND5; 12), HpPPAT ( PDB ID: 3NV7; 13), BpPPAT ( PDB ID: 3K9W ; 14), CbPPAT ( PDB ID: 4F3R; unpublished), PaPPAT ( PDB ID: 3X1J; 15) and MaPPAT ( PDB ID: 5O06 As indicated by the structure of AbPPAT with CoA ( PDB ID: 5YH7), the ligand binding cleft
59 5ts2 3pxu Structural and biochemical studies of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with dephospho-coenzyme A and coenzyme A 2019 A Gupta, PK Singh, P Sharma, P Kaur, S Sharma- International journal of, 2019 - Elsevier pseudolamelli (BpPPAT, PDB ID: 3PXU), Mycobacterium abcessus (MaPPAT, PDB ID: 5O08) and Pseudomonas aeruginosa (PaPPAT, PDB ID: 5TS2 Therefore, structure of enzyme, PPAT must be determined from the bacterium against whom specific drug has to be designed
60 5ts2 3pxu Phosphopantetheine Adenylyltransferase: A promising drug target to combat antibiotic resistance 2020 A Gupta, P Sharma, TP Singh, S Sharma- Biochimica et Biophysica Acta, 2020 - Elsevier Although, the DPCK domain of the human fusion protein shows high sequence and structural homology to bacterial DPCK The PDB IDs of the structure , percentage sequence identities and rms deviations for the C atoms are also indicated ... The structures of complexes of PPAT with dPCoA from several bacterial species have been determined so far and include EcPPAT (PDB ID: 1B6T), MtPPAT (PDB ID: 3RBA), BpPPAT (PDB ID: 3PXU), MaPPAT (PDB ID: 5O08), PaPPAT (PDB ID: 5TS2) and AbPPAT (PDB ID: 5ZZC
61 2lwk - Supporting Information for Occurrences of protonated base triples in RNA are determined by their cooperative binding energies and specific functional 2021 A Halder, A Jhunjhunwala, D Bhattacharyya, A Mitra - biorxiv.org Figure S1: Context of occurrences of G(CC) H:+ Trans/W:W Cis triple (System 2). 2D representation of (A) the 5S rRNA, (B) Domain III of 25S rRNA of S. cerevisiae and (C) HDV ribozyme are shown and the structural motifs that contain (G) 3D structure of the PDB : 3KIR Chain: A
62 3pgz 3lgj MODIFIED HELICASES 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 ...
63 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 ...
64 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)
65 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
66 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
67 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
68 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
69 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
70 3meq - Reaction and protein engineering employing a carbonyl reductase from candida parapsilosis 2012 A Jakoblinnert, UDMB Ansorge-Schumacher - 2012 - d-nb.info ... Four X-ray templates were selected for modeling the CPCR1 structure (349aa): Yeast ADH I from S. cerevisiae with bound trifluorethanol (347 residues with quality score 0.522, PDB ID 2HCY), ADH from Brucella melitensis (341 residues with quality score 0.590, PDB ID 3MEQ), ...
71 4x54 - The mycolic acid reductase Rv2509 has distinct structural motifs and is essential for growth in slowgrowing mycobacteria 2020 A Javid, C Cooper, A Singh, S Schindler- Molecular, 2020 - Wiley Online Library structures of the four highest-scoring experimental SDRs (3ASU/3ASV, 1XG5, 4X54 and 4BMV based on the SDR from Sphingobium yanoikuyae (4BMV. pdb ; GenBank ID ACB78183.1 structure elements of Rv2509 aligned to its corynebacterial homologues, the core structure of
72 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 ...
73 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
74 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. ...
75 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
76 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
77 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
78 3lgj 3pgz Modified enzymes 2018 AJ Heron, RV Bowen, M Bruce- US Patent App. 15, 2018 - Google Patents In order to assess whether a suitable protein structure exists to use as a template to build a protein model, a search is performed on the protein data bank ( PDB ) database The sequence alignment and template structure are then used to produce a structural model of the The polynucleotide binding motif may be selected from any of those shown in Table 5 below. Bartonella 3LGJ, Q6G302 homo-tetramer
79 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
80 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.
81 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
82 6c87 6byq SIMBAD: a sequence-independent molecular-replacement pipeline 2018 AJ Simpkin, F Simkovic, JMH Thomas- Section D: Structural, 2018 - scripts.iucr.org researchers involved. All cases involve the crystallization of a known contaminant. Examples involving the use of SIMBAD for novel structure solution are available elsewhere, such as PDB entries 6byq, 6c87 and 5wol. Cases illustrating
83 3gwc - PREDICTION OF BINDING ENERGIES/INTERACTIONS BETWEEN DIOSPYRIN AND DIFFERENT TARGET PROTEINS OF Mycobacterium tuberculosis BY IN SILICO MOLECULAR DOCKING STUDIES 2014 AJ Suresh, R Devi, KM Noorulla - Indo American Journal of Pharmaceutical Research, 2014 - ejmanager.com ... Protein Data Bank (PDB) ID were selected, NADH-dependent enoyl- ACP reductase (InhA) - 2NSD, Adenosine kinase (Adok) - 2PKK, Mycolic acid synthase (PcaA) - 1L1E, Lysine N- acetyltransferase (MbtK) - 1YK3, Thymidylate synthase X (ThyX) - 3GWC, Thymidylate kinase ...
84 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
85 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 ...
86 4k9d - Network-Pharmacology and DFT Based Approach Towards Identification of Leads from Homalomena aromatica for Multi-Target In-Silico Screening on Entamoeba 2020 AK Goswami, HK Sharma, N Gogoi- Current Drug, 2020 - ingentaconnect.com The 3D model of EhGAPDH was predicted based on multiple templates ( PDB IDs: 4O59, 4K9D , 1U8F, 4Z0H, 3V1Y) It uses robust, cross-validated Quantitative Structure Toxicity Relationship (QSTR) models for assessing various measures of toxicity. 3.6
87 4maq - The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria 2018 AKH Weiss, JR Loeffler, KR Liedl- Biochemical Society, 2018 - biochemsoctrans.org Skip to main content. Main menu. Home; About the Journal: Scope; Editorial Board; Benefits of Publishing; Impact & Metrics; Advertising/Sponsorship; About the Biochemical Society. Current Issue; For Authors: Submit Your Paper; Submission
88 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
89 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 ...
90 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.
91 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 ...
92 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
93 5u29 - Sntese, elucidao estrutural e estudos in silico de novos compostos 2-amino-tiofnicos imdicos candidatos a frmacos antifngicos, antileishmanicida e 2019 ALC Pereira - 2019 - repositorio.ufpb.br Synthesis, structural elucidation and in silico studies of novel 2-amino- thiopheneic compounds imidic hybrids were synthesized with determined physicochemical characteristics and confirmed structures through 1H CYP51A1 ( PDB id: 1EA1); (B): ESBT-06 e FTAs ( PDB id: 3SFX
94 3i4e - Three enzymes and one substrate; regulation of flux through the glyoxylate shunt in the opportunistic pathogen, Pseudomonas aeruginosa. 2018 AL Crousilles, SK Dolan, P Brear, DY Chirgadze- bioRxiv, 2018 - biorxiv.org IDH active site architecture with that of ICD in the AceK-ICD complex from E. coli ( PDB ; 3LCB) reveals that X-ray Diffraction, Structure Determination, and Refinement ICL, IDH and ICD were solved using the structural templates 3I4E (to be published), 4ZDA (to be published) and
95 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: ...
96 5unb - Universal architectural concepts underlying protein folding patterns 2018 A Lesk, R Subramanian, L Allison, D Abramson- bioRxiv, 2018 - biorxiv.org to give proteins their intricate three-dimensional shapes and folding patterns (tertiary structure ) Unravelling protein architecture and discovering the relationship among these three major levels of of protein folding patterns have revealed recurrent themes at all structural levels (2
97 4ni5 - Structure-guided stereoselectivity inversion of a short-chain dehydrogenase/reductase towards halogenated acetophenones 2016 A Li, L Ye, X Yang, C Yang, J Gu, H Yu - Chemical Communications, 2016 - pubs.rsc.org ... As a powerful method to decipher a possible molecular basis for enzyme properties, structuralcomparison involving the detailed structure alignment has ... using SDRs from Drosophilamelanogaster (31% identity, PDB: 1SNY A) and Brucella suis (48% identity, PDB: 4NI5 A) as ...
98 3fdz - SYSTEM AND USES FOR GENERATING DATABASES OF PROTEIN SECONDARY STRUCTURES INVOLVED IN INTER-CHAIN PROTEIN INTERACTIONS 2010 AL Jochim, PS Arora - US Patent App. 12/753,638, 2010 - Google Patents ... 4, 2010 Sheet 5 of 7 US 2010/0281003 Al EXTRACT PROTEIN STRUCTURES WITH GREATER THAN TWO ENTITIES FROM PDB PROTEIN DATA BANK ASSIGN SECONDARY STRUCTURE ACCORDING TO (() AND vj/ANGLES OF PROTEIN BACKBONE CALCULATE ...
99 4tyz - PROTEIN-PROTEIN INTERACTIONS OF HUMAN PARVOVIRUS B19 NS1 AND IDENTIFICATION OF THE NS1 TRANSCRIPTIONAL TRANSACTIVATION DOMAIN 2018 AL Morano - 2018 - repository.arizona.edu Page 1. PROTEIN-PROTEIN INTERACTIONS OF HUMAN PARVOVIRUS B19 NS1 AND IDENTIFICATION OF THE NS1 TRANSCRIPTIONAL TRANSACTIVATION DOMAIN Structure: Residues 112-214 share 32% sequence identity to x-ray crysal structure in PDB file 4TYZ chain A (a protein of unknown function).
100 5deo - Novel antimycobacterial compounds suppress NAD biogenesis by targeting a unique pocket of NaMN adenylyltransferase 2019 AL Osterman, I Rodionova, X Li, E Sergienko- ACS chemical, 2019 - ACS Publications ADVERTISEMENT. Log In Register. Cart. ACS; ACS Publications; C&EN; CAS. ACS Publications: ACS Journals; ACS eBooks; C&EN Global Enterprise. A; Accounts of Chemical Research; ACS Applied Bio Materials; ACS Applied Electronic
101 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
102 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<
103 3fvb - Towards reverse engineering of Photosystem II: Synergistic Computational and Experimental Approaches 2014 A Mahboob - 2014 - dr.library.brocku.ca ... 62 3.4.3. Comparison of water channels found in this work to channelsobtained from static structures ..... ... 19 Figure 1.2 Structure of PSII dimershowing subunits CP47,D1,D2,cyt b559,CP43,cyt c550 ...
104 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. ...
105 4ncx - Parallelization of large-scale Drug-Protein binding experiments 2017 A Makris, D Michail, I Varlamis- & Simulation (HPCS, 2017 - ieeexplore.ieee.org ... pair of proteins 4M10 (the structure of Murine Cyclooxygenase-2 Complex with Isoxicam) and 3KQZ (the structure of a ... random motifs malaria motifs 4fm5 42 6cox 27 3kwb 7 4ncx 23 1cjb 25 1nnu 10 1d3z 3 1cmx ... correspond to protein chains, only the distinct PDB IDs were kept. ...
106 3u04 - Molecular modeling of Plasmodium falciparum peptide deformylase and structure-based pharmacophore screening for inhibitors 2016 A Manhas, SP Kumar, PC Jha - RSC Advances, 2016 - pubs.rsc.org ... PDB entry, Organism, Resolution (), Metal ion, E-Value, Identity ... 5, 3U04, Ehrlichia chaffeensis,1.70, Zn 2+, 3 10 28, 37. ... actinonin complex created from superimposition was manually editedto replace with the Fe 2+ ion to generate the PfPDFFe 2+ actinonin complex structure ...
107 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. ...
108 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 ...
109 4gl8 - Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter 2017 AM Groshong, A Dey, I Bezsonova, MJ Caimano- mBio, 2017 - Am Soc Microbiol Structural features distinguish BbOppA4 from Gram-negative and Gram-positive OBPs.We took advantage of the crystal structure of BbOppA4 ( PDB ID: 4GL8 ) (39) to determine if B. burgdorferi OBPs possess structural elements compatible with promiscuous peptide binding, the
110 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
111 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
112 5ts2 - Umbrella Sampling and X-ray Crystallographic Analysis Unveil an Arg-Asp Gate Facilitating Inhibitor Binding Inside Phosphopantetheine Adenylyltransferase 2018 A Mondal, R Chatterjee, S Datta- The Journal of Physical, 2018 - ACS Publications In this study, we have attempted to further comprehend the structural details and mechanisms involved in AcCoA binding Material and method: MD simulations The PPATWT-AcCoA structure used for this study was obtained from RCSB- PDB ( PDB ID: 3X1J)
113 4qji - Natural products encompassing antituberculosis activities 2020 A Monga, A Sharma- Studies in Natural Products Chemistry, 2020 - Elsevier The structure and composition of the cell envelope of M. tuberculosis are distinguished from that of other kinds of prokaryotes S. No. PDB ID, Title, Anti-TB agents 1OY0, Pantothenate kinase, 1e. 4QJI , Phosphopantothenate-cysteine ligase, Phosphopantetheine
114 4k9d - Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora 2021 AM Perez, JA Wolfe, JT Schermerhorn, Y Qian- RSC Advances, 2021 - pubs.rsc.org The PDB validation server shows this structure to be typical of structures of comparable resolution in measures of R and number of Ramachandran, sidechain and real-space R-value Z score (RSRZ) outliers ( PDB ID 6PX2) The model used for molecular replacement was 4K9D
115 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 )
116 4qhq - Navigating Among Known Structures in Protein Space 2019 A Narunsky, N Ben-Tal, R Kolodny- Computational Methods in Protein, 2019 - Springer evolutionary history, with sequences that diverged beyond the point where one can identify their common ancestry; for example, the SCOP fold, CATH Architecture , and ECOD As both neighbors ( pdb 4qhq and pdb 3qwl) have a bound methionine in their PDB structure (Fig
117 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
118 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
119 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
120 3hzu 3hwi Mycobacterium tuberculosis CysA2 is a dual sulfurtransferase with activity against thiosulfate and 3-mercaptopyruvate and interacts with mammalian cells 2019 AN Meza, CCN Cambui, ACR Moreno, MR Fessel- Scientific reports, 2019 - nature.com dimensional structures of M. tuberculosis CysA2 ( PDB code 3HIW, yellow), CysA3 ( PDB code 3AAY, red) and SseA ( PDB code 3HZU , blue) Based on the available three-dimensional structure of CysA2, we performed a comparison with putative orthologues studied in the
121 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)
122 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%).
123 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
124 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
125 5vm8 - Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites 2020 AP Perlinska, A Stasiulewicz- PLOS Computational, 2020 - journals.plos.org depicted with rainbow coloring (TrmD, PDB ID: 4yvg), (B) unknotted methyltransferase (Trm5, PDB ID: 2zzm On the top of this it was shown that the structure of the knotted core Different conformations of the ligand imply differences in both structural and chemical characteristics of
126 3ek2 - Structural insights into Staphylococcus aureus enoyl-ACP reductase (FabI), in complex with NADP and triclosan 2010 A Priyadarshi, EEK Kim? - Proteins: Structure, Function, and Bioinformatics, 2010 - Wiley Online Library ... A. aeolicus FabI (PDB ID 2P91) in green, M. tuberculosis FabI (PDB ID 3FNH) in light green, B. napus FabI (PDB ID 1D7O) in cyan, E. coli FabI (PDB ID 2FHS) in pink, P. falciparum FabI (PDB ID 2OP1) in red, B. pseudomallei FabI (PDB ID 3EK2) in orange, and B. anthracis FabI ...
127 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
128 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
129 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
130 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
131 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 ...
132 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 ...
133 3laa 3la9 Recent advances in the understanding of trimeric autotransporter adhesins 2019 AR Kiessling, A Malik, A Goldman- Medical Microbiology and Immunology, 2019 - Springer ring (Orange) domains. c Top view of Hia BD1( PDB ID:1S7M) rep- resenting tryptophan side chain from each monomer. d Structure of BpaA ( PDB ID: 3LAA ) representing FGG (Violet purple), short neck (Olive), head (Teal), long neck (Blue) domains
134 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. ...
135 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
136 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
137 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 ...
138 3inn - Substrate-induced closing of the active site revealed by the crystal structure of pantothenate synthetase from Staphylococcus aureus 2010 A Satoh, S Konishi, H Tamura, HG Stickland? - Biochemistry, 2010 - ACS Publications ... entry 2EJC) and the ATP complex structure of a protein annotated as PS of Brucella melitensis (PDB entries 3INN). In general, the PS protomer can be divided into two domains (N- and C-terminal domains), with the active site located at the interface of these domains. ...
139 3tsm - Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa-decarboxylation is not essential for indole formation 2020 A Sderholm, MS Newton, WM Patrick- Journal of Biological, 2020 - ASBMB catalytic residues taking part in the dehydration step are harder to speculate on due to the substantial structural rearrangements taking However, a different open conformation of helix 0 is observed in the structure of IGPS from Brucella melitensis ( PDB 3TSM , unpublished
140 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
141 4o6r - Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus 2015 AS Halavaty, RL Rich, C Chen, JC Joo… - … Section D: Biological …, 2015 - scripts.iucr.org ... DALI (Holm & Rosenstro¨ m, 2010) analysis found a putative ALDH from Burkholderia cenocepacia (PDB entry 4o6r; Seattle Structural Genomics Center for Infectious Disease, unpublished work) to be the closest structural homolog of SaBADH (Z-score of 59.6; r.m.s.d. of 1.3 A ° ; 38% sequence homology)...
142 5upg - The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical 2018 A Sharma, V Kumar, S Pratap, P Kumar- International journal of biological, 2018 - Elsevier Similarly, a crystal structure of LpxC from P. aeruginosa complexed with the LpxC-4 inhibitors (PDB ID: 5UPG) have also shown the interactions of ligand at these two sites.
143 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 ...
144 3ecd 3h7f Structural adaptation of serine hydroxymethyltransferase to low temperatures 2010 A Siglioccolo, F Bossa, S Pascarella - International journal of biological Macromolecules, 2010 - Elsevier ... Table 5. List of representative structures of SHMT currently available in the Protein Data Bank. PDB id Resolution (Å) Biological source 3ECD 1.60 Burkholderia pseudomallei. ...
145 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. ...
146 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 ...
147 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 ...
148 4iuj - The influenza virus polymerase complex: an update on its structure, functions, and significance for antiviral drug design 2016 A Stevaert, L Naesens - Medicinal Research Reviews, 2016 - Wiley Online Library ... Closeup showing a superposition of the crystal structures of the PAC-PB1N interface[223] (PDB: 3CM8) on that of the FluA polymerase (light gray) and the apo form of PAC[224] (light blue; PDB: 4IUJ). ...
149 4odj 4h3z, 4kgn, 4ig6 Static and dynamic properties of knotted biopolymers: from bulk to nanochannels and nanopores 2017 A Suma - 2017 - iris.sissa.it ... Several pioneering experiments and structural surveys demonstrated that knots can appear in biopolymers such as RNA [7], proteins [8 ... PDB download (~105 protein chains) ... We have used the same cutoff distance to check if some structure , such as the cyclotide, had a cyclized ...
150 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). ...
151 2lwk - Prediction of RNA 1H and 13C chemical shifts: a structure based approach 2013 AT Frank, SH Bae, AC Stelzer - The Journal of Physical Chemistry …, 2013 - ACS Publications ... which 1 H and 13 C chemical shifts data were acquired, and a structural description. ... each chemicalshift entry was mapped to local 3D descriptors calculated from PDB coordinates. ... 1 H chemicalshifts for the nuclei corresponding to those in our chemical shift-structure database. ...
152 4p8r 4lsm Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa 2018 ATP Machado, M Silva, J Iulek- et Biophysica Acta (BBA)-Proteins and, 2018 - Elsevier cruzi (glicosomal) ( PDB : 4LSM) [12], Trypanosoma brucei (glicosomal) ( PDB : 4P8R ) [13], Leishmania 3PYM), Homarus americanus ( PDB : 1GPD) [46] and Escherichia coli ( PDB : 1GAD) [47 general, they are similar, with some differences in secondary structure elements; RMSD
153 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 ...
154 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
155 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)
156 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
157 3k9h - Molecular anatomy of ParA-ParA and ParA-ParB interactions during plasmid partitioning 2015 A Volante, JC Alonso - Journal of Biological Chemistry, 2015 - ASBMB ... Superimposition of full-length monomer structures of δ (in green) and T thermophilus Soj (ParA-Sm) in blue (PDB: 2BEK); with P1-ParA in yellow (PDB: 3EZ6); and with TP228-ParF (ParA-Sm) in orange (PDB: 3K9H)...
158 3rih 3uve The Role of Charged Residues in the Structural Adaptation of Short-Chain Alcohol Dehydrogenase (SDR) from Thermophilic Organisms to High Temperatures 2018 AV Popinako, MY Antonov, EY Bezsudnova- Moscow University, 2018 - Springer Protein structures from PDB database are marked with asterisk 3RIH (Mycobacterium Abscessus tion involving specific patterns of the distribution of dif- ferent residues in the structure , including their distribu- tion on the solvent-accessible molecular surface and in the protein core
159 4yk1 4yk3, 4yk2 Versatility of the BID domain: Conserved function as type-IV-secretion-signal and secondarily evolved effector functions within Bartonella-infected host cells 2019 A Wagner, C Tittes, C Dehio- Frontiers in microbiology, 2019 - frontiersin.org BID fold is highlighted through superposition of the three solved BID domains: BroBep6_tBID1 (green; PDB : 4YK1 ), BclBep9_tBID1 (cyan; PDB : 4YK2), and BheBepE_BID1 (purple; PDB : 4YK3 into ancestral tBIDs found in the canonical FIC-OB-BID architecture and derived
160 4npc - Synthesis and antibacterial activity of novel icariin derivatives 2019 A Wang, Y Xu- Die Pharmazie-An International Journal of, 2019 - ingentaconnect.com The X-ray structure of MetAP1 ( PDB : 4npc ) was also obtained from Protein Databank ( PDB ). Before going to the docking procedure, the protein structure was prepared using the Protein preparation wizard of the DS 2017 R2
161 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
162 3md0 - Structure-function relationships of the G domain, a canonical switch motif 2011 A Wittinghofer, IR Vetter - Annual review of biochemistry, 2011 - annualreviews.org ... Two structures of putative ArgK proteins have been solved by structural genomics (2www,3md0), which have an ExxG motif instead of DxxG and alpha-helical N- and C-terminal extensions ...
163 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 ...
164 3la9 - Structure and biology of trimeric autotransporter adhesins 2011 A ?yskowski, JC Leo, A Goldman - Bacterial Adhesion, 2011 - Springer ... The structures are identified by their PDB ID codes where avail- able. ... structure of Haemophilus HiaDB2; (c) 3emi: structure of Haemophilus Hia 307?442 non-adhesive domain; (d) 3emo: structure of transmembrane domain of Haemophilus Hia 973?1098; (e) 3la9: structure of ...
165 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
166 6x79 7jv2 Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors 2021 Baysal, N Abdul Ghafoor, RS Silme, AN Ignatov- PloS one, 2021 - journals.plos.org The 3' end of the genome encodes 4 major structural proteins, including the spike protein (S), the nucleocapsid protein structure of refusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation ( PDB : 6X79 ), and X-ray diffraction structure of SARS
167 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 ...
168 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
169 4j3g - Non-specific activities of the major herbicide-resistance gene BAR 2017 B Christ, R Hochstrasser, L Guyer, R Francisco- Nature plants, 2017 - nature.com We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism... The search model was an ensemble model generated with Ensembler using eight protein structures homologous to BAR (PBD codes and % identity to BAR: 2JLM (28%), 3DR8 (35%), 4J3G (31%), 4JXQ (33%), 4MBU ...
170 2lwk - RNA on the move: the plasmodesmata perspective 2018 BC Reagan, EE Ganusov, JC Fernandez, TN McCray- Plant Science, 2018 - Elsevier While this synthetic RNA consists of only 32 nucleotides, it has a corresponding radius of gyration of 15.48 Å (1.548 nm) when bound to the small molecule DPQ (6,7-dimethoxy-2-(piperazin-1-yl)quinazolin-4-amine) (PDB ID: 2LWK)
171 4lsm - O proteoma estrutural anterior ao ltimo ancestral universal comum e suas implicaes para a evoluo das primeiras protenas 2017 B DO , I Jernimo - 2017 - rei.biblioteca.ufpb.br With the accretion of the new parts in the structure , the catalytic function emerged. Also it is suggested that the initial structural motifs RMSD: Root-Mean-Square Deviation (Raiz do Desvio Quadrtico Mdio) PDB : Protein Data-Base (Banco de Dados de Protenas)
172 3tzs 3tf6 Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides 2015 BE Allred, PB Rupert, SS Gauny… - Proceedings of the …, 2015 - National Acad Sciences ... molecules from available crystal structures (the structures described in this work plus PDB (41)accession ... 1 × 8U, 3FW4, 3FW5, 3HWE, 3HWF, 3HWG, 3K3L, 3PEC, 3PED, 3TF6, 3TZS, 3UOD,and ... of key calyx residues, colored as in H, isolated from the 73-structure superposition ...
173 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. ...
174 3h7f - Phylogenetic framework and molecular signatures for the main clades of the phylum actinobacteria 2012 B Gao, RS Gupta - Microbiology and Molecular Biology Reviews, 2012 - Am Soc Microbiol ...Structures of the S-adenosyl-l-homocysteine hydrolase (PDB accession number 3CE6) (240) (A and B) and serine hydroxymethyltransferase (PDB accession number 3H7F) (C and D) proteins from M. tuberculosis showing the locations in protein structures of the 9-aa and 5-aa actinobacterium-specific inserts that are found in these proteins...
175 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),
176 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
177 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...
178 4qhq - Structural insights into the substrate specificity of SP_0149, the substrate-binding protein of a methionine ABC transporter from Streptococcus pneumoniae 2019 B Jha, R Vyas, J Bhushan, D Sehgal- Section F: Structural, 2019 - scripts.iucr.org Z-score Rmsd (A ) Nalign %seq} Bound substrate PDB code Protein name and description 15.2 1.36 223 41 Met 4qhq A nutrient-binding protein (bound to methionine in the Sequence identity in SSM is calculated from structure (three-dimensional), rather than sequence
179 3dmo 3krb, 3kxq, 3myb, 3p4t, 3gvg, 3mx6, 3ecd, 3f0d, 3hgb, 3krs, 3p0t, 3r1i, 3lb5, 3fvb, 3k2c, 3pe8, 3qat, 3nwo, 3oec, 3meb, 3ii9, 3e7d, 3ndn, 3ngf, 3cxk, 3qxz, 3moy, 3n5o, 3pk0, 3ngj, 3oks, 3ek2, 3i3f, 3gwc, 3oj6, 3lr4, 3oj7, 3k9w, 3ld3, 3enk, 3h7f, 3h81, 3oa3, 3pgx, 3ipw, 3oc9, 3qh4, 3fs2, 3k31, 3gbz, 3eg4, 3lnc, 3nfw, 3p2y, 3kzu, 3dms, 3quv, 3gwa, 3lqw, 3mpz, 3njd, 3lv0, 3p32, 3r6f, 3ol3, 3qbp, 3ndo, 3nrr, 3qd5, 3qlj, 3mqd, 3o38, 3js4, 3o0m, 3qhx, 3gp3, 3js5, 3mdx, 3mxu, 3fq3, 3o0k, 3pzy, 3md7, 3mqw, 3o0h, 3eiz, 3kzx, 3ixc, 3oc7, 3kre, 3l3b, 3qk8, 3gir, 3laa, 3mc4 Rare Sidechain Conformations in Proteins and DNA 2015 BJ Hintze - 2015 - search.proquest.com ... Ponder and Richards in 1987 (Ponder and Richards, 1987), and they are important. tools in structural biology (Dunbrack, 2002). ... the Protein Data Bank ( PDB ) (Berman, 2000). ... 2010; Winn et al., 2011), protein structure prediction and design (Bower et al., 1997; ...
180 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 . ...
181 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
182 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
183 2kn9 - Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry 2017 BK Maiti, RM Almeida, I Moura, JJG Moura- Coordination Chemistry, 2017 - Elsevier Rubredoxins (Rds) and their derivatives have been extensively used, in the last few decades, in order to elucidate structure and functional aspects of metal sit.
184 3enk - Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non- 2010 B Manavalan, SK Murugapiran - BMC structural , 2010 - bmcstructbiol.biomedcentral.com ... The structure of the VR (PDB code 2p4h; 310 residues) and a dTDP-glucose 4,6-dehydratase(PDB code 1r6d; 322 residues) showed ... In addition, we used 2p4h as the baseline point andsuperimposed it onto the PDB structures listed in Table 1. The root-mean-square ... 3enk. ...
185 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
186 3iml - Structure and function study of the complex that synthesizes S-adenosylmethionine 2014 B Murray, SV Antonyuk, A Marina, SM Van Liempd - IUCrJ, 2014 - journals.iucr.org ...(b) Superposition of apo-MAT([alpha]2)2 from Burkholderia pseudomallei (PDB entry 3iml , Baugh et al., 2013[Baugh L. et al. (2013). Plos One, 8, e53851.], in pink) with the SAMe-bound MAT([alpha]2)2 (PDB entry 2p02 in blue);...
187 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 ...
188 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
189 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
190 3o0h - Structure function studies of enzymes involved in scavenging ROS in Oryza sativa to avoid abiotic stress 2015 B Pani - 2015 - krishikosh.egranth.ac.in ... analysis against PDB (http://www.rcsb.org/) to identify suitable templates for ... The pair-wise 3-D structural alignment and RMSD of the equivalent C atoms, of the model and template was performed using MATRAS (MArkovianTRAnsition of Structure evolution) web ...
191 5j3b - Structure and Function of an Elongation Factor P Subfamily in Actinobacteria 2020 B Pinheiro, CM Scheidler, P Kielkowski, M Schmid- Cell Reports, 2020 - Elsevier In order to gain insights into the structural configuration of this Actinobacteria EF-P, we X-ray crystal structure to 2.2- resolution (for data processing and structure refinement statistics its overall folding topology with the previously reported bacterial EF-P structures and consists of
192 5j3b - The translation elongation factor P in actinobacteria 2020 B Pinheiro Damasceno Florentino - 2020 - edoc.ub.uni-muenchen.de NC Nascent peptide-chain ORF Open reading frame PCR Polymerase chain reaction PDB Protein data EF- P facilitates translation of XPPX motifs is based in many structural studies... Structural superposition and ribbon representations of available EF-P structures. C. glutamicum (PDB code 6S8Z, orange, this work), Acinetobacter baumannii (PDB code: 5J3B, blue), E. coli (
193 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
194 3rd5 - Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR) 2016 BRK Menon, SJO Hardman, NS Scrutton - of Photochemistry and , 2016 - Elsevier ... A putative uncharacterized SDR protein (PDB id: 3RD5) that has the highest sequence identitywith POR was used as the reference structure and the sieving procedure removed 68% of the3RD5 residues at 1.8 sieving level using Mustang-MR sieving server. ...
195 2n6g 2myy, 2lpd Structures of a nonribosomal peptide synthetase module bound to MbtH-like proteins support a highly dynamic domain architecture 2016 BR Miller, EJ Drake, C Shi, CC Aldrich- Journal of Biological, 2016 - ASBMB The crystal structure of an MLP from Pseudomonas aeruginosa called PA2412 (13), and the from M. tuberculosis (14) and three other organisms [M. marinum (2MYY), M. avium ( 2N6G ), and Burkholderia 2LPD)] that have not been published, all show a flat architecture with three
196 3rqi - Molekulare Charakterisierung der Interaktion der Sensorkinase ETR1 aus Arabidopsis thaliana mit nachgeschalteten Komponenten des Ethylensignalwegs 2012 B Scharein - 2012 - docserv.uni-duesseldorf.de ...Die strukturelle Information für Phospho‐Aspartat stammen aus dem Antwort Regulator Protein aus Burkholderia pseudomallei (pdb‐code 3RQI) ...
197 3rqi - Phosphorylation alters the interaction of the Arabidopsis phosphotransfer protein AHP1 with its sensor kinase ETR1 2011 B Scharein, G Groth - PloS one, 2011 - dx.plos.org ... form. A homology model of AHP1 built on the crystal structure of the Hpt protein OsHP1 from rice (PDB code 1YVI) which is shown in Figure 5 further supports our experimental data that AHP1 forms homodimers in solution. The ...
198 3gtd 3tv2, 3rd8, 3rrp, 3qbp, 3ome, 3oc7, 3njb, 3njd, 3myb, 3moy, 3he2, 3h81, 4qfe Stereochemistry of enzymatic water addition to C= C bonds 2015 BS Chen, LG Otten, U Hanefeld - Biotechnology Advances, 2015 - Elsevier ... Entry, Name (EC-number), Sources (PDB-number), Types of reaction, Cofactor, Regio- andstereoselectivity. ... sapiens (3E04) Mycobacterium abscessus (3RRP) Sinorhizobium meliloti (4HGV)Thermus thermophilus (1VDK) Rickettsia prowazekii (3GTD) Mycobacterium tuberculosis ...
199 4dz4 - The neighboring subunit is engaged to stabilize the substrate in the active site of plant arginases 2020 B Sekula- Frontiers in plant science, 2020 - frontiersin.org It is worth noting that the structure of agmatinase from Deinococcus radiodurans ( PDB ID: 1WOG) (Ahn et al., 2004) is ID: 3LHL), agmatinase from Thermoplasma volcanium (TvAGM, PDB ID: 3PZL), and agmatinase from Burkholderia thailandensis (BtAGM, PDB ID: 4DZ4 )
200 4xk1 - Structural analysis of phosphoserine aminotransferase (isoform 1) from Arabidopsis thalianathe enzyme involved in the phosphorylated pathway of serine 2018 B Sekula, M Ruszkowski, Z Dauter- Frontiers in Plant Science, 2018 - ncbi.nlm.nih.gov identity (Supplementary Figure S2), which are structurally very similar to AtPSAT1: PaPSAT ( PDB ID: 4xk1 , rmsd = 1.0 For example, in the structure of HsPSAT ( PDB ID: 3e77), the N-terminal coil at first look Residues 816 visible in the structure came from the expression tag
201 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
202 6nb4 6nb7 Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19) 2020 B Shanmugaraj, K Siriwattananon- Asian Pac J Allergy, 2020 - apjai-journal.org PDB ID 6CS2)72 and the following antibodies are shown in magenta: 80R ( PDB ID 2GHW)73, F26G1 ( PDB ID 3BGF)74, m396 ( PDB ID 2DD8)75, and S230 ( PDB ID 6NB7 (P D B ID 6NB4 ) Structure of SARS coronavirus spike receptor- binding domain complexed with receptor
203 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. ...
204 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
205 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
206 3r1i - Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii 2014 BS Shah, SG Tetu, SJ Harrop, IT Paulsen… - Structural Biology and …, 2014 - journals.iucr.org ... [Figure 2], Figure 2 Structure of SDR ... 4g81 ; pale red), 3-oxoacyl-(ACP) reductase (Synechococcuselongatus FabG2; PDB entry 4dmm ; pale green), 3-oxoacyl-(ACP) reductase (S. aureus FabG3;PDB entry 3osu ; pale blue), M. marinum SDR (PDB entry 3r1i ; pale yellow ...
207 4j3g - PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS 2019 B Strauss - 2019 - scholarworks.sjsu.edu set. Validated residue binary assignments of 0 (no change in secondary structure ) and 1 (change in secondary structure ) were determined (DSSP) from 3D X-ray structures for sets of virtually identical chains crystallized under different conditions
208 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. ...
209 3rih 3uve The Role of Charged Residues in the Structural Adaptation of Short-Chain Alcohol Dehydrogenase (SDR) from Thermophilic Organisms to High Temperatures 2018 Bulletin of Moscow University. Series 2. Chemistry, 2018 - cyberleninka.ru PDB (*), 3RIH (Mycobacterium Abscessus*) 2,36 2,36 1,32 7,62 8 THE ROLE OF CHARGED RESIDUES IN THE STRUCTURAL ADAPTATION OF SHORT-CHAIN
210 4eqy - Structure-Based Virtual Screening of Pseudomonas aeruginosa LpxA Inhibitors Using Pharmacophore-Based Approach 2020 BV Bhaskar, TMC Babu, A Rammohan, GY Zheng- Biomolecules, 2020 - mdpi.com 1J2Z) [22], Leptospira interrogans ( PDB ID: 3HSQ) [23] and Burkholderia thailandensis ( PDB ID: 4EQY ) [24] were In this study, the PaLpxA structure was superimposed on LpxA orthologs from different bacterial Organism PDB ID Monomer A Monomer B RMSD () Pocket Size (
211 4f3p - Molecular and structural basis of glutathione import in Gram-positive bacteria via GshT and the cystine ABC importer TcyBC of Streptococcus mutans 2013 B Vergauwen, K Verstraete? - Molecular Microbiology, 2013 - Wiley Online Library ... binding protein HisJ of Salmonella enterica (Oh et al., 1994; Yao et al., 1994), D177 and R96 in the arginine-binding protein of Salmonella typhimurium (Stamp et al., 2011), and D180 and R98 in the glutamine-binding protein of Burkholderia pseudomallei (PDB code: 4F3P). ...
212 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),
213 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. ...
214 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 ...
215 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
216 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
217 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
218 5dld 4hwg UDP-N-acetilglicosamina 2-epimerase de Staphylococcus aureus: estrutura, dinmica e prospeco de novos ligantes 2020 C Azevedo - teses.usp.br the crystallographic structure of the enzyme to characterize conformational changes as they 45 Figura 13 Estrutura cristalogrfica da cadeia A da protena UDP-GlcNac 2-epimerase de S. aureus ( PDB : 5ENZ), com uma molcula de UDP em stio ativo, vista de frente (A) e
219 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
220 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. ...
221 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
222 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
223 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 ...
224 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 ...
225 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 ...
226 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
227 4o3v 4nhf, 4lso, 4kz1 VirB8-like protein TraH is crucial for DNA transfer in Enterococcus faecalis 2016 C Fercher, I Probst, V Kohler - Scientific , 2016 - ncbi.nlm.nih.gov ... A structure-based homology search revealed that TraH is related to proteins of the VirB8 family,which all exhibit a ... PDB code 4NHF, 14% sequence identity), Bartonella quintana (PDB code 4LSO,6% sequence identity), Rickettsia typhi (PDB code 4O3V, 19% sequence ...
228 3ifg - The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions 2010 CG Langendorf, TLG Key, G Fenalti, WT Kan? - PloS one, 2010 - dx.plos.org ... Shortly after the human SSADH structure was published, the structure of SSADH from Burkholderia pseudomallei, without a substrate or cofactor (PDB ID: 3ifg and 3ifh), was deposited into the PDB by the Seattle Structural Genomic Centre for Infectious Disease. ...
229 3lg6 - Molecular dynamics for computational proteomics of methylated histone H3 2014 C Grauffel, RH Stote, A Dejaegere - Biochimica et Biophysica Acta (BBA)- …, 2014 - Elsevier ... This analysis is made possible by the substantial amount of structural information available oncomplexes between PHD domains and modified histone tails. ... Protein Data Bank IDs are indicated,and NMR structures are labeled with a (*). Protein name, Ref. ... PDB structure. ...
230 3k2c - Supplementary material to GISA: Using Gauss Integrals to identify rare conformations in protein structures 2019 C Grnbk, T Hamelryck, P Rgen - 2019 - biorxiv.org The rar2 scoring method scans for structures having a distribution of words significantly different from that found in the old, here set to 7 ngstrm; the E chain of the 2er7 structure is disqualified for this reason, but 7> means that in the PDB -file the chain id was left blank 14
231 5upg - Widening the Therapeutic Window: Time-Dependent Inhibitors of LpxC and InhA for Treating Multidrug-Resistant Bacterial Infections 2018 C Gu - 2018 - search.proquest.com 46 Figure 2.10. X-ray crystal structure of paLpxC in complex with PF5081090 ( 5UPG . pdb ). ... 48 PD Pharmacodynamics PDB Protein Data Bank PIPES Piperazine-N,N-bis(2-ethanesulfonic acid) Sfp Phosphopantetheinyl transferase SKR Structure -kinetic relationship
232 2n6x - RNA structure refinement using NMR solvent accessibility data 2017 C Hartlmller, JC Gnther, AC Wolter, J Whnert - Scientific , 2017 - ncbi.nlm.nih.gov ... Figure 4b ) and the corresponding sPRE values are underestimated based on the NMR solution structure , independent of which structural model of the UUCG loop motif ( PDB codes 1HLX, 1K2G, 1TLR, 1Z31, 2KHY, 2KOC, 2KZL, 2LHP, 2LUB and 2N6X ) was used. ...
233 2kwl - The coenzyme A disulphide reductase of Borrelia burgdorferi is important for rapid growth throughout the enzootic cycle and essential for infection of the mammalian host 2011 CH Eggers, MJ Caimano, RA Malizia? - Molecular Microbiology, 2011 - Wiley Online Library ... The orientation is the same as Fig. 3 published in (Wallen et al., 2008). PDB code for the BaCoADR structure used is 3CGD. B. The predicted active site of BbCoADR. BbCoADR residues [Cys 42 (chain A) and Tyr366' and Tyr424' (chain B)] are indicated. ...
234 6d9y 6d9n Protein secondary structure online server predictive evaluation 2019 - Chinese Journal of Bioinformatics, 2019 - search.ebscohost.com 1 SPIDER Fig.1 Main structure of SPIDER 2.1
235 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 ...
236 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
237 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
238 4ijn - Sugar analog synthesis by in vitro biocatalytic cascade: A comparison of alternative enzyme complements for dihydroxyacetone phosphate production as a 2017 CJ Hartley, NG French, JA Scoble, CC Williams- PloS one, 2017 - journals.plos.org of pH 7.09.0 and between 2537C. Most of the selected enzymes had known crystal structures (those with ATP-recycling enzymes, two acetate kinases (AceK) from Mycobacterium smegmatis and Methanosarcina thermophila (AceK Ms ; WI_011727188; PDB 4IJN and AceK
239 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)
240 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
241 2ko7 - Structure-based Computational analysis of Protein Binding sites for Function and Druggability in Macrophage Infectivity Potentiator (MIP) Protein of Legionella pneumophila 2013 CK Naidu, Y Suneetha - Current Trends in Biotechnology & Pharmacy, 2013 - search.ebscohost.com ... with rapamycin protein (mip) (PDB ID: 2VCD) (Ceymann et al., 2008) was retrieved from the proteindata bank (PDB). ... PDB ID Protein Name ... 2KO7 Chain A Solution structure of peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with Cycloheximide- N ...
242 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 ...
243 3uf8 - Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus 2014 C Leyrat, M Renner, K Harlos, JT Huiskonen? - Structure, 2013 - Elsevier ... HMPV M was solved at 2.8 ? resolution by molecular replacement using the structure of RSV M (Protein Data Bank ID [PDB ID] 2VQP; sequence identity, 38%). Data collection and refinement statistics are given in Table 1 (R work = 0.19; R free = 0.23). Table 1. ...
244 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 ...
245 5vog 4mh4 Phase Combination and its Application to the Solution of Macromolecular Structures: Developing ALIXE and SHREDDER 2018 CL Milln Nebot - 2018 - tdx.cat Table 1 Test set for performance evaluation of SHREDDER and ALIXE... ID PDB 5VOG solvent content
246 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).
247 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 ...
248 4mpq - Structural Characterisation of members of the DHDPS/NAL subfamily of proteins 2017 C MacDonald - 2017 - ir.canterbury.ac.nz 2HMC A. tumefaciens HypD 4MPQ B. melitensis HypD p(r) Pair distribution function plot pdb Protein data base This information is displayed using espript software (Robert and Gouet 2014) with secondary structure of E. coli DHDPS being shown along the top
249 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
250 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 ...
251 3hhe 3uw1, 3u7j, 3s5p Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118 2012 CMC Lobley, P Aller, A Douangamath? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... (2006). Acta Cryst. F62, 427-431.] ), Bartonella henselae (PDB entry 3hhe ; Seattle Structural Genomics Center for Infectious Disease, unpublished work), Vibrio vulnificus YJ016 (Kim et al., 2009 [Kim, TG, Kwon, TH, Min, K., Dong, M.-S., Park, YI & Ban, C. (2009). Mol. ...
252 3rd7 3u0a Mycobacteria encode active and inactive classes of TesB fatty-acyl CoA thioesterases revealed through structural and functional analysis 2017 CMD Swarbrick, GV Bythrow, DG Arago - Biochemistry, 2017 - ACS Publications ... Our structural homology analysis revealed that at least one other TesB acyl-CoA thioesterasealso contains an Ala residue at the active site, while two other ... The TesB thioesterase from M. avium (MaTesB) is a 276-amino acid protein and shares a low level of sequence similarity with the homologous TesB thioesterases from ... the orthologous TesB thioesterase from M. avium (PDB entry 3RD7, 41%).. ...
253 3rd7 3u0a Structural and functional characterization of TesB from Yersinia pestis reveals a unique octameric arrangement of hotdog domains 2015 CMD Swarbrick, ME Perugini, N Cowieson… - Biological …, 2015 - journals.iucr.org ... marinum; however, a further two structures have been solved and annotated as TesB thioesterasesfrom M. avium (PDB entries 3rd7 and 4r9z ... Thus, much of the current understanding regarding thisclass of thioesterases been built on the E. coli structure, with the other ...
254 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)
255 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
256 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. ...
257 5dd7 - Structural and functional analysis of thiaminephosphate and homoserine kinases from Mycobacterium tuberculosis 2016 CM Ntui - 2016 - repository.up.ac.za Figure 3.17 X-ray diffraction pattern obtained from ThiL crystal Figure 3.18 The overall structure of MtbThiL Figure 3.20 Crystals obtained from optimization with ThrB Figure 4.1 Structural topology of MtbThiL with other ThiL structures PDB Protein Data Base pI Isoelectric point
258 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
259 5i7w - Omega transaminases: discovery, characterization and engineering 2019 CM Palacio - 2019 - rug.nl (7), who grouped the enzymes in superfamilies by structural similarities and named the superfamilies after the PLP enzyme of which the crystal structure was determined first. The PLP fold-type classification system of Grishin et al Brucella suis, pdb 5I7W )
260 3ek2 - Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase 2017 C Neckles, S Eltschkner, JE Cummings - Biochemistry, 2017 - ACS Publications ... Structural analysis of nine enzyme:inhibitor complexes reveals that the variation in structure kinetic relationships can be rationalized by structural rearrangements of bpFabI1 and subtle changes to the orientation of the inhibitor in the binding pocket. ...
261 3ek2 - Rational Optimization of Diphenyl Ether Binding Kinetics to the Enoyl-ACP Reductase FabI1 from Burkholderia pseudomallei 2017 C Neckles, S Eltschkner, JE Cummings- Biochemistry, 2017 - ncbi.nlm.nih.gov 35 The structures were solved by molecular replacement with Phaser 36 utilizing either the apo structure of bpFabI1 ( PDB entry 3EK2 ), or the complex structure of bpFabI1 with PT155 ( PDB entry 4BKU) as search model
262 6nb6 - Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies 2020 CO Barnes, AP West Jr, KE Huey-Tubman- Cell, 2020 - Elsevier Share. Export. Advanced. Cell Cell. Volume 182, Issue 4, 20 August 2020, Pages 828-842.e16. Journal home page for Cell. Article. Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies
263 6wps - Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies 2020 CO Barnes, CA Jette, ME Abernathy, KMA Dam- bioRxiv, 2020 - ncbi.nlm.nih.gov 1g) that were isolated from the same donor 5 . They share structural similarities with each other and with other VH353/short 1) and C144 Fab (from C144-S structure ) aligned on a RBD monomer. ACE2 ( PDB 6M0J; light green surface) is aligned on the same RBD for reference ... Composite model of C135-RBD (blue and gray, respectively) overlaid with the SARS-CoV-2 NAb S309 (sand, PDB 6WPS) and soluble ACE2
264 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).
265 3kzx 3p96 Sequence-and structure-based approaches to deciphering enzyme evolution in the Haloalkonoate Dehalogenase superfamily 2014 C Pandya - 2014 - open.bu.edu ... , all , + and /20. Importantly, ~10% of domain combinations in the Protein Data Bank(PDB) are domain insertions. ... It performs structure-based alignment and secondary-structure comparison to identify conserved and inserted secondary structural elements. ...
266 6auj 3ix6, 3gwc Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS) 2019 C Pozzi, L Lopresti, G Tassone, S Mangani- Molecules, 2019 - mdpi.com This review is aimed to summarize the current understanding of structure and function of bTSs and FDTSs and the recent id 1F4B [17]), Brucella melitensis (BmTS; PDB id 3IX6, unpublished research), and Elizabethkingia anophelis (EaTS; PDB id 6AUJ , unpublished research
267 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. ...
268 5umh 5vxt Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch 2018 CR Schlachter, L Daneshian, J Amaya- Insect biochemistry and, 2018 - Elsevier Here, we have determined the spectroscopic, structural and metabolic properties of TuIDRCD, the first arthropod ID-RCD used for determination, refinement, and validation of mTuIDRCD structure ; however, in this case the structure of mbp-(t48)TuIDRCD ( PDB code: 5VG2
269 5umh - Structural and Functional Studies of Proteins from the Agricultural Pests Tetranychus Urticae and Aspergillus Fumigatus 2017 C Schlachter - 2017 - scholarcommons.sc.edu Structural homologs of TuDioxygenase identified by the Dali server [51] were dioxygenases such as: SACTE_2871 (PDB code 4ILT, 153/155 residues aligned, RMSD 1.8 Å); catechol 1,2-dioxygenase from Burkholderia multivorans (PDB code 5UMH, 167/307 residues aligned
270 3ke1 - Torsion Angle Preferences in Druglike Chemical Space: A Comprehensive Guide 2013 C Sch?rfer, T Schulz-Gasch, HC Ehrlich? - Journal of medicinal ?, 2013 - ACS Publications ... The growing number of entries in the Cambridge Structural Database (CSD)(19) and the ProteinData Bank (PDB)(20) allow derivation of more and more reliable and specific rules, and efficient tools exist to do this.(21, 22) Here we present ... PDB entry 3ke1(39) exemplifies ...
271 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. ...
272 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
273 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 ...
274 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)...
275 3ecd - Single-stranded oligonucleotides can inhibit cytokine production induced by human toll-like receptor 3 2008 CT Ranjith-Kumar, KE Duffy, JL Jordan? - Molecular and cellular biology, 2008 - Am Soc Microbiol ... (C) The locations of peptides P1 and P2 within the three-dimensional model of 3ECD (PDB accession number, 1ZIW). The peptide spanning residues 211 to 222 is in green, and the one spanning residues 560 to 583 is in yellow. ...
276 3upt - Systematic analysis of the sequence-structure-function relationships of thiamine diphosphate-dependent enzymes 2015 C Vogel - 2015 - elib.uni-stuttgart.de ... A putative acetohydroxyacid synthase (AHAS) from the yeast Torulaspora delbrueckii (TdAHAS, sid|11616) and a transketolase from Agrobacterium tumefaciens (AtTK, sid|29832), both missing experimentally determined structure information, were modeled using the structures of ScAHAS (pdb|1N0H, Pang et al. 2004) and the transketolase from Burkholderia pseudomallei (BpTK, pdb|3UPT, Baugh et al. 2013) as templates, respectively.e ...
277 5cy4 - Structural basis of small RNA hydrolysis by oligoribonuclease (Cps ORN) from Colwellia psychrerythraea strain 34H 2019 CW Lee, SH Park, CS Jeong, SS Cha, H Park- Scientific reports, 2019 - nature.com Structure alignment search using DALI server showed that CpsORN exhibited high structural similarity with ORN HinORN; PDB code 1J9A), and Acinetobacter baumannii (AbaORN; PDB code 5CY4 ), and XC847 from Xanthomonas campestris (XcaORN; PDB code 2GBZ
278 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
279 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 ...
280 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
281 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
282 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. ...
283 3kc6 3khw Structure and Function of Influenza Virus Ribonucleoprotein 2018 CY Lo, YS Tang, PC Shaw- Virus Protein and Nucleoprotein Complexes, 2018 - Springer These structures include PDB : 2VY7, 2VY8, 3KC6 , 3KHW, 2GMO (solution structure of NLS-domain). Structures composing of both domains are also available ( PDB : 2VY6, 3CW4) (Tarendeau et al. 2007; Tarendeau et al. 2008; Kuzuhara et al. 2009; Yamada et al
284 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. ...
285 4wkw - The redox state regulates the conformation of Rv2466c to activate the antitubercular prodrug TP053 2015 D Albesa-Jov, N Comino, M Tersa, E Mohorko - Journal of Biological , 2015 - ASBMB ...E, schematic representation showing the comparison between the crystal structure of Rv2466c-CT-His and the structural homologue from M. leprae (PDB code 4WKW). The canonical thioredoxin folds are shown in orange. The α-helical subdomains of Rv2466c-CT-His and the M. leprae homologue ...
286 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. ...
287 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. ...
288 3enk - Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme 2014 D Armstrong - 2014 - etheses.whiterose.ac.uk ... the protein structure. POR isoforms in plants are also notable as components of the prolamellarbodies (PLBs), large paracrystalline structures that are precursors to the thylakoid ... similar structuralfeatures, leading to the production of a structural model for POR. A unique ...
289 3e7d - POLYPEPTIDES FOR USE IN SELF-ASSEMBLING PROTEIN NANOSTRUCTURES 2016 D Baker, JB Bale, NP King - US Patent , 2016 - freepatentsonline.com ... panel B) comprise 12 pentamers (dark grey) and 30 dimers (light grey), and the I32-28 designmodel and crystal structure (panel C ... Starting proteins were those derived from pentameric, trimeric,and dimeric crystal structures from the Protein Data Bank (PDB), along with a ...
290 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 ...
291 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
292 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
293 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
294 3glq - Structural insight into binding mode of inhibitor with SAHH of Plasmodium and human: interaction of curcumin with anti-malarial drug targets 2016 DB Singh, S Dwivedi - Journal of chemical biology, 2016 - Springer ... Structural superimposition. MatchMaker module of UCSF Chimera 1.9 was used to create asuperposition of PDB structures [14]. ... The six SAHH structure from human (1LI4), P. falciparum(1V8B), M. tuberculosis (2ZJO), B. pseudomallei (3GLQ), T. brucei (3H9U), and B ...
295 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 ...
296 3hm0 - Thioesterases: A new perspective based on their primary and tertiary structures 2010 DC Cantu, Y Chen, PJ Reilly - Protein Science, 2010 - Wiley Online Library ... If a crystal structure is known, the Protein Data Bank (PDB, http://www.rcsb.org) accession code also appears. ThYme will be continuously updated: the content of each family will grow as GenBank, UniProt, and PDB do. ... Family, Fold, RMSD ave (?), P ave (%), PDB files. ...
297 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
298 4pca - Structure and Biophysical Characterization of the S-adenosylmethionine Dependent O-methyltransferase PaMTH1, a Putative Enzyme Accumulating during … 2015 D Chatterjee, D Kudlinzki, V Linhard, K Saxena… - Journal of Biological …, 2015 - ASBMB ... α2 Page 7. Structure and Biophysical characterization of PaMTH1 7 loop ... Arg232, Asp235).CCoAOMT (Medicago sativa) is (PDB:1SUI) one of the closest structural homologueof PaMTH1 and also crystallizes as a dimer. The dimerization ...
299 2kok 2mu0 Structure and function prediction of arsenate reductase from Deinococcus indicus DR1 2019 D Chauhan, PA Srivastava, V Agnihotri- Journal of molecular, 2019 - Springer Model1 of ArsC with 3RDW is 1.5 , 1I9D is 2.2 , 1J9B is 2.2 , 2KOK is 3.0 In the case of ArsC, the ArsC C12S mutant ( PDB ID: 1S3C) from E. coli was used as the a confidence score of 0.9040, indicating a very high quality model, where an accurate modeled structure has a
300 4pca 4oa5, 4oa8 Outer Membrane Protein OmpB Methylation May Mediate Bacterial Virulence 2017 DCH Yang, AH Abeykoon, BE Choi, WM Ching- Trends in Biochemical, 2017 - Elsevier ... on methylation of bacterial OMPs has uncovered novel mechanisms with respect to protein structure and catalytic ... of the 226-residue dimeric O-methyltransferase have been determined in its apo form ( PDB ID:4OA8) and in complex with AdoMet (4OA5) or AdoHcy ( 4PCA ). ...
301 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. ...
302 3oks - Single active‐site mutants are sufficient to enhance serine: pyruvate α‐transaminase activity in an ω‐transaminase 2015 D Deszcz, P Affaticati, N Ladkau, A Gegel… - FEBS …, 2015 - Wiley Online Library ... More distantly related ω-TAms identified in the structure alignments, such as ornithine-AT (PDBcode: 1OAT), 4-aminobutyrate-AT (PDB code: 3OKS and 1SFF), acetylornithine-AT (PDB code:2ORD), l-lysine-epsilon-AT (PDB code: 2CJG), β-phenylalanine-AT (PDB code ...
303 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 ...
304 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 ...
305 3cez - On the functionality of a methionine sulfoxide reductase B from Trypanosoma cruzi 2020 DG Arias, MS Cabeza, ML Echarren- Free Radical Biology, 2020 - Elsevier These enzymes can reduce specifically one or another of the isomers of MetSO (free and protein-bound). This redox modification could change the structure and function of many proteins, either concerned in redox or other metabolic pathways ... Models were based on the resolved structure of MSRB from Methanothermobacter thermautotrophicus (PDB 2K8D), Burkholderia pseudomallei (PDB 3CEZ), and Xanthomonas campestris (PDB 3HCI).
306 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
307 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
308 3iew - Synthesis and Computational Analysis of Novel IspF Inhibitors 2018 D Harper, M Rouffet, L Votapka- Bulletin of the American, 2018 - pointloma.whdl.org The crystal structure of IspF was taken from the Protein Data Bank, code 3iew .7 The first As for the protein, the monomer's crystal structure was cleaned and protonated with the H++ webserver (version 3.2).11 The . pdb file was manually edited to correct these protonation states
309 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
310 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
311 3tde 3iml, 5t8s The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase 2019 D Kleiner, F Shmulevich, R Zarivach, A Shahar- Journal of molecular, 2019 - Elsevier MAT ( PDB ID), Phylum/class, Monomer length b, % sequence identity to E. coli, Interface c, M. tuberculosis ( 3TDE ), Actinobacteria/actinobacteria, 403, 59%, large, 11.5, 1983, 23, 11 1). In addition, the flexible loops (positions 89116) fully discernible in this structure were found
312 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,
313 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 ...
314 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.
315 2khp - NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY IN THE STUDY OF PROTEIN-LIGAND INTERACTIONS 2018 DL Morris - 2018 - rave.ohiolink.edu Structures of target proteins were obtained from the Protein Data Bank (PDB). The PBD code for BrmGRX is 2KHP and hGRX1 is 1JHB.
316 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 ...
317 3gaf - The three-dimensional structure of Clostridium absonum 7-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP (H) 2016 D Lou, B Wang, J Tan, L Zhu, X Cen, Q Ji - Scientific reports, 2016 - ncbi.nlm.nih.gov ... They are Brucella Melitensis 7-HSDH with no ligand (PDB code: 3GAF) at resolution 2.20 and Escherichia coli 7-HSDH (EC 7-HSDH; PDB code: 1FMC ... As one of the SDRs, with thesimilar structure to the two 7-HSDHs above, CA 7-HSDH possesses the ...
318 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). ...
319 3d5t - Structures of citrate synthase and malate dehydrogenase of Mycobacterium tuberculosis 2015 DM Ferraris, R Spallek, W Oehlmann… - Proteins: Structure, …, 2015 - Wiley Online Library ... thermophilus (4KDE), Thermus flavus (1BDM), Aquaspirillum articum (1B8P), and Burkholderiapseudomallei (3D5T). ... RMSD = 1.4 Å) and malate dehydrogenase from T. flavus (PDB code =1BMD ... The structure of M. tuberculosis malate dehydrogenase shows the presence of a ...
320 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]. ...
321 4f2n - Three Alkaloids from an Apocynaceae Species, Aspidosperma spruceanum as Antileishmaniasis Agents by In Silico Demo-case Studies 2020 D Morales-Jadn, J Blanco-Salas, T Ruiz-Tllez- Plants, 2020 - mdpi.com of this method can provide insights into the druggable targetome contained in the structural proteome criteria were chosen (vg to be a starting structure , to have a similar structure of a drawn using Marvin Sketch 19.15 converting the format of some structures into pdb files using ... Table A2. Enzymes crystal structures available in PDB server. 4f2n.1.A target SOD
322 6q04 - Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity 2021 D Pal- Journal of Structural Biology, 2021 - Elsevier The structural and dynamics analyses of the Spike show that its fusion loop spatially organizes three fusion peptides contiguous to each other to synergistically I propose a Contact Initiation Model based on the architecture of the Spike quaternary structure that explains the
323 3fs2 3ez4, 3ijp Targeting multiple targets in Pseudomonas aeruginosa PAO1 using flux balance analysis of a reconstructed genome-scale metabolic network 2011 D Perumal, A Samal, KR Sakharkar… - Journal of drug …, 2011 - Taylor & Francis ... 3D structural information of target protein–ligand molecular complexes is a very usefulmethod to identify high-quality drug targets. ... A search against Protein Data Bank (PDB)helped us shortlist targets that had structure available. ...
324 3fvb 4di0 Understanding the Encapsulins 2015 D Radford - 2015 - tspace.library.utoronto.ca ....The Dps-like bacterioferritin-like family was defined as the set of proteins similar to the Brucella melitensis biovar Abortus 2308 bacterioferritin [PDB accession: 3FVB] .. Lastly the rubrerythrin-like family was defined as the set of proteins similar to the Burkholderia pseudomallei rubrerythrin [PDB accession: 4DI0], and N-terminal domains of the Ferroglobus placidus DSM 10642 encapsulin ...
325 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
326 3qi6 3qhx The hyperthermophilic cystathionine -synthase from the aerobic crenarchaeon Sulfolobus tokodaii: expression, purification, crystallization and structural insights 2017 D Sato, T Shiba, S Mizuno, A Kawamura - Section F: Structural , 2017 - scripts.iucr.org ... E. Ahmed & S. Gourinath, unpublished work) and Mycobacterium ulcerans Agy99 (PDB entries 3qi6 and 3qhx ... of StCGS was solved by molecular replacement using E. coli CGS (PDB entry 1cs1 ...at basic pH and elevated temperature is caused by changes in the protein structure. ...
327 3qi6 - Structural and mechanistic insights into homocysteine degradation by a mutant of methionine lyase based on substrateassisted catalysis 2017 D Sato, T Shiba, S Yunoto, K Furutani - Protein , 2017 - Wiley Online Library ... Cys116 remains connected to the 2*/3* loop to form the active center. We previouslydemonstrated that the crystal structure of PpMGL is a ... 1e5f, 3acz and 5dx5), cystathionine-synthases (PDB: 1cs1 and 3qi6) and cystathionine -lyases (PDB: 1n8p and 2nmp). ...
328 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.
329 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. ...
330 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 ...
331 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.
332 3i4e - Silencing Motifs in the Clr2 Protein from Fission Yeast, Schizosaccharomyces pombe 2014 D Steinhauf, A Rodriguez, D Vlachakis, G Virgo… - PloS one, 2014 - dx.plos.org ... forcefield. The crystal structure of the Haloalkane Dehalogenase (PDB entry: 3QNM) was used for the modeling of C2SM1. Likewise ... the C2SM2. Finally, the Isocitrate Lyase (PDB entry: 3I4E) was used for the modeling of C2SM3. The sequence ...
333 3dmp 3hm0, 3e5b, 3qbp Tetramer protein complex interface residue pairs prediction with LSTM combined with graph representations 2020 D Sun, X Gong- Biochimica et Biophysica Acta (BBA)-Proteins and, 2020 - Elsevier The structure diagram of LSTM neural network is shown in Fig. 3. (See Fig. 1, Fig Table 1. Dataset. DataSet, PDB ID 2H8N, 2JBR, 2NQO, 2Y32, 3DFQ, 3ESI, 3G7K, 3HM0, 3OHP, 3RD4, 3 V15, 1IZ1, 1JL2. 1KAM, 1NSW, 2GJD, 2R90, 2ZYZ, 3CDK, 3CO2, 3DMP , 3F6Z, 1BV4, 1YIF
334 4ix8 - Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies 2021 D Suplatov, Y Sharapova, V vedas- Multiple Sequence Alignment, 2021 - Springer etc.): 3WGB, 2W7E, 3A2B, 1IBJ, 1LKC, 1 V72, 2BKW, 2EZ2, 4IX8 , 1QZ9, 4BA5 The missing loop regions in these PDB structures were reconstructed using the MODELLER software [23] enzymes, the MATT algorithm was used to prepare the initial 3D- structure superimposition of -- This is not a duplicate of their earlier 2018 work
335 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 ...
336 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). ...
337 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 ...
338 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
339 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
340 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 ...
341 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
342 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 ...
343 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
344 4wxt - Reposicionamento de frmacos para malriaum mtodo que identifica alvos no domnio das doenas negligenciadas 2015 E Barante - 2015 - arca.icict.fiocruz.br ... the know-how of many technological areas, with focus on information, computing, and, particularlyon the construction and use of existing Internet databases such as MEDLINE, PubMed and PDB. ...The problems appear by the lack of textual structure or appropriate markup tags. ...
345 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
346 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 ...
347 3tmg - The GbsR family of transcriptional regulators: functional characterization of the OpuAR repressor 2018 E Bremer, S Ronzheimer, B Warmbold- Frontiers in, 2018 - frontiersin.org the linker region, an aromatic cage is predicted as the inducer-binding site, whose envisioned architecture resembles that subtilis GbsR protein (Nau-Wagner et al., 2012); it is based on the crystal structure of the DNA-binding protein Mj223 of M. jannaschii ( PDB entry 1KU9
348 5jry - Molecular Mechanisms of Bacterial Bioluminescence 2018 E Brodl, A Winkler, P Macheroux- Computational and Structural, 2018 - Elsevier we also show stick models of the substrate analog (indole-3-acetaldehyde – blue) and the cofactor (NADP+ − grey) in the respective binding sites obtained from the superposition of the LuxC model with indole-3-acetaldehyde dehydrogenase from Pseudomonas syringae (PDB 5IUW) and from the structure of an aldehyde dehydrogenase from Burkholderia multivorans (PDB 5JRY), respectively.
349 3lgj - Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34 2017 E Cernooka, J Rumnieks, K Tars, A Kazaks- Scientific reports, 2017 - nature.com Structural homologs of the ORF6 protein were identified using the Dali server ... the number of superimposed atoms were ... 59 (PDB ID: 3LGJ) and 58 (PDB ID: 3VDY)
350 4q6u - PAS domains in bacterial signal transduction 2021 EC Stuffle, MS Johnson, KJ Watts- Current Opinion in Microbiology, 2021 - Elsevier ad) PAS monomer structures : (a) The PAS structural prototype photoactive dimer bound to heme cofactor (Fe 3+ , PDB : 4HI4, [25]) and a liganded monomer with cyanomet heme (Fe 3+ -CN, PDB : 3VOL, [31 For clarity, b-type heme is only shown bound to the liganded structure
351 3kw3 - The structure of alanine racemase from Acinetobacter baumannii 2014 E Davis, E Scaletti-Hutchinson - Section F: Structural , 2014 - scripts.iucr.org ... Alanine racemase, PDB entry, Whole monomer #, N-terminal domain +, C-terminal domain , Active site ##. Alr Eco, 2rjg, 1.30 (41%), 1.32 (40%), 1.02 (43%), 0.65 (60%). Alr Bhe, 3kw3, 1.86 (29%), 1.68 (25%), 1.07 (36%), 0.91 (48%). ...
352 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), ...
353 3tl6 - Statistical Analysis of Protein Structural Features: Relationships and PCA Grouping 2014 E Del Prete, S Dotolo, A Marabotti - Intelligence Methods for , 2014 - Springer ... 1ODK, 1PK9, 1QE5, 1TCU, 1V4N, 1VMK, 1XE3, 1Z33, 2P4S, 3KHS, 3OZE, 3SCZ, 3TL6, 3UAV,4D98 ... The legend of the right refers to PDB codes (see Table 1) with the addition ... to con- sidersome structural features as putative markers of the peculiar structure-function properties ...
354 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
355 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
356 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
357 3gaf - New microbial hydroxysteroid dehydrogenases and their synthetic application for the selective modification of bile acids. 2011 EE Ferrandi - 2011 - insubriaspace.cineca.it ... but it has been hypothesized that binding of bile acids to hydrophobic pocket(s) of the proteasesmay destabilize their structure, making additional ... Bile salts are used for the structural rigidity ofthe steroid skeleton, which allows the formation of stable cavities, and because both ...
358 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
359 6nb7 6ws6, 6wpt, 6wps, 6nb8 Structural basis of SARS-CoV-2 and SARS-CoVantibody interactions 2020 E Gavor, YK Choong, SY Er, H Sivaraman- Trends in, 2020 - Elsevier While the binding of COV21 to the S-glycoprotein resembles the binding of the SARS-CoV S230( PDB : 6NB7 )[73], the binding interface SARS-CoV-2-S-S309-Fab[12] complex ( PDB : 6WPS/6WPT/6WS6) and the crystal structure of SARS
360 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 ...
361 5dwn - Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex 2017 EJ Loveridge, C Jones, MJ Bull, SC Moody - Journal of , 2017 - Am Soc Microbiol ... protein [37], including conservation of the bleomycin-binding regions), phosphinothricinN-acetyltransferase (36% identical to phosphinothricin N-acetyltransferase from Brucella ovis[GenBank accession number WP_006155257; PDB accession number 5DWN], with significant ...
362 4lgv - Molecular Cloning and Exploration of the Biochemical and Functional Analysis of Recombinant Glucose-6-Phosphate Dehydrogenase from Gluconoacetobacter 2019 EJ Ramrez-Nava, D Ortega-Cuellar- International journal of, 2019 - mdpi.com Keywords: glucose 6 phosphate dehydrogenase (G6PD); bioinformatics analysis; kinetic parameters; thermal stability; three-dimensional structure Finally, using homologous 3D structures , we modeled the G6PD protein, which suggests the structural and functional
363 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).
364 3obk - The Remarkable Character of Porphobilinogen Synthase 2016 EK Jaffe - Accounts of Chemical Research, 2016 - ACS Publications ... (c) The pro-octamer dimer of T. gondii PBGS (PDB id 3obk) includes the ... (d) Three subunits ofthe yeast PBGS octamer (PDB id 1ohl ... All known PBGSs are homomultimers, and various multimersdiffer in quaternary structure interactions that govern enzymatic activity by impinging ...
365 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 ...
366 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. ...
367 3gp5 - Structure and Activity of the Metal-independent Fructose-1, 6-bisphosphatase YK23 from Saccharomyces cerevisiae 2010 E Kuznetsova, L Xu, A Singer, G Brown, A Dong? - Journal of Biological Chemistry, 2010 - ASBMB ... of YK23 was solved to 1.75-? resolution using selenomethionine-substituted protein and multiple wavelength anomalous dispersion (PDB code 3F3K ... 2a6p; Z-score 23.7; rms deviation 1.9 ?), the phosphoglyceromutase GpmA from Burkholderia pseudomallei (3gp5; Z-score ...
368 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 ...
369 3pk0 3rih Structural and functional characterization of the aminoacetone utilization microcompartment from Mycobacterium smegmatis MC2 155 2019 E Mallette - 2019 - atrium.lib.uoguelph.ca P)(H) - nicotninamide adenine dinucleotide (phosphate)(reduced) NTP - nucleotide triphosphate PDB - protein data bank (protein structure archive) PDU 1.2.1 Superstructure Architecture Microcompartments were first visualized in electron micrographs of carboxysome
370 3rih 3pk0 Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis 2018 E Mallette, MS Kimber- Biochemistry, 2018 - ACS Publications We determined the structure of APDH in both apo form (at 1.7 ) and as a ternary enzyme complex with NADP + and aminoacetone... This work has shown that 3PK0 (APDHMSM0779) is an orthologue, and analysis (see below) suggests that 3RIH is also likely a Mycobacterial APDH orthologue
371 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
372 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. ...
373 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
374 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
375 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
376 6x79 - Structure-based design of a highly stable, covalently-linked SARS-CoV-2 spike trimer with improved structural properties and immunogenicity 2021 E Olmedillas, CJ Mann, W Peng, YT Wang, RD Avalos- bioRxiv, 2021 - biorxiv.org For VFLIP_D614G, a population of 213,852 particles yielded a 2.8 resolution structure (Figure S2). Importantly, the density maps confirm Further sub-classification revealed an overall architecture that is similar to other closed spikes in the Protein Data Bank ( PDB ). ... A previously published structure of the SARS-CoV-2 ectodomain with all RBDs in the down conformation (PDB ID 6X79) was used to fit the cryo-EM maps in UCSF ChimeraX
377 3ke1 4dxl, 4ed4, 4emd, 3q8h Molekulare Erkennung in chemischen und biologischen Systemen 2015 E Persch, O Dumele, F Diederich - Angewandte Chemie, 2015 - Wiley Online Library ... c) Bindungsmodus der Liganden 27 und 28 im Komplex mit BpIspF (27: 2.05 Å Auflösung, PDB ID: 3KE1; 28: 1.75 Å Auflösung, PDB ID: 3Q8H). ...
378 3ke1 4emd, 4ed4, 4dxl, 3q8h Molecular Recognition in Chemical and Biological Systems 2015 E Persch, O Dumele, F Diederich - … Chemie International Edition, 2015 - Wiley Online Library ... c) Cocrystal structure of ligand 12 bound to TGT (1.68 Å resolution, PDB ID: 3RR4)51 and d ...reorganization of the protein and the changes in the water network solvation occurring upon minorchanges in the ligand structures.52 Without high-resolution structural information, a ...
379 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
380 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
381 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
382 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 ...
383 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
384 4tmd - Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis 2017 E Sviridova, P Rezacova, A Bondar, V Veverka - Scientific , 2017 - ncbi.nlm.nih.gov ... Structural similarity searches revealed that none of the deposited structures in the Protein DataBank ... Using the DALI server, the best fit was obtained for the crystal structure of the hypotheticalprotein MSMEI_5302 from Mycobacterium smegmatis (PDB: 4TMD), an Rv0999 ...
385 4ffc 3r4t Novel-Substituted Heterocyclic GABA Analogues. Enzymatic Activity against the GABA-AT Enzyme from Pseudomonas fluorescens and In Silico Molecular 2018 E Tovar-Gudio, JA Guevara-Salazar- Molecules, 2018 - mdpi.com -Aminobutyric acid (GABA) is the most important inhibitory neurotransmitter in the central nervous system, and a deficiency of GABA is associated with serious neurological disorders. Due to its low lipophilicity, there has been an intensive search for new molecules with increased
386 3r4t 4ffc Novel-Substituted Heterocyclic GABA Analogues. Enzymatic Activity against the GABA-AT Enzyme from Pseudomonas fluorescens and in Silico Molecular Modeling 2018 E Tovar-Gudio, J Guevara-Salazar, J Bahena-Herrera- Molecules, 2018 - mdpi.com molecular docking studies to explain their inhibitory character based in different structural and electronic to the concept of molecular similarity, which states that molecules with similar structure will have Figure 6 shows the cavity of the GABA-AT ( PDB : 1SF2 from Escherichia coli
387 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). ...
388 3cxk - Unraveling the specificities of the different human methionine sulfoxide reductases 2014 E Vandermarliere, B Ghesquire, V Jonckheere - , 2014 - Wiley Online Library ... In a first step, all human protein structures determined by X-ray crystallography were retrieved from the Protein Data Bank (PDB) [30]. ... With the aid of a BLAST search [33] against the PDB, the possible templates were shortlisted and PDB-entry 3CXK [34] was chosen as a ...
389 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
390 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
391 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),...
392 4eqy - Structures of Pseudomonas aeruginosa LpxA Reveal the Basis for Its Substrate Selectivity 2015 EW Smith, XJ Zhang, C Behzadi, LD Andrews - Biochemistry, 2015 - ACS Publications ... Superimposition of all three monomers from the biologically relevant homotrimer, showing loops L1 and L2. (D) P. aeruginosa LpxA monomer superimposed onto eight ortholog LpxA monomeric structures (E. coli (PDB ID: 1LXA), B. thailandensis (PDB ID: 4EQY), ...
393 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
394 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).
395 3u0g - Structural insight into the substrate specificity of PLP fold type IV transaminases 2020 EY Bezsudnova, VO Popov, KM Boyko- Applied Microbiology and, 2020 - Springer Due to the rigid structure of the -sheet, the residues constituting it form a peculiar mold for substrate binding. The interdomain loop (light blue) and -turn (black) of the large domain of the first subunit confine the P-pocket from the other sides PDB ID:*. X-strand 3U0G
396 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
397 4nbr - PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations 2021 F Adasme-Carreno, J Caballero- Journal of Chemical, 2021 - ACS Publications Inf. Model. 2021, 61, 4, 1789-1800. ADVERTISEMENT. RETURN TO ISSUEPREVComputational Chemis...Computational ChemistryNEXT. Journal Logo. PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations
398 3men - Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives 2013 F Andreoli, A Jorge Moura Barbosa - Current , 2013 - ingentaconnect.com ... Current Pharmaceutical Design, 2013, Vol. 19, No. 4 583 Table 1. Available 3D Structure ofHuman and Bacterial HDACs Class Name Organism PDB ID Ligand Domain Reference ... [262]Bacterial APAH Burkholderia pseudomallei 3MEN Catalytic Domain [263] a PDB ligand ID ...
399 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
400 3hzg - Synthse d'analogues nuclotidiques visant l'inhibition de la Thymidylate Synthase Flavine-Dpendante 2018 F Chevrier - 2018 - tel.archives-ouvertes.fr PCF2 : gem-Difluoromthylphosphonate PDB : Protein data bank pH : Potentiel hydrogne 18 Page 20. 19 I. Les bactries : structures et mcanismes d'infection Schma 1 : Structure gnrale d'une bactrie. Cependant, elles possdent des attributs essentiels leur survie
401 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
402 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
403 4fur - Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences 2016 FD Richard, R Alves, AV Kajava - Bioinformatics, 2016 - Oxford Univ Press ... Examples of proteins where TRs found in sequence either correspond to (A) presence (PDBcode 3VN3 (Kondo et al., 2011)) or (B) absence (4FUR) of TRs ... both in sequence and in structure(TR-SS) and 'false' TRs only found in sequence but not in the structure (TR-SNS ...
404 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
405 3md7 - The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold 2011 F Fernandez, F Garces, M L?pez-Estepa? - BMC evolutionary biology, 2011 - biomedcentral.com ... Furthermore, the recently determined structure of a MBL from Brucella melitensis subsp. abortus (PDB ID 3md7 and structures thereof) (unpublished) has revealed a monomeric enzyme with an Mn2+-dependent active site similar to UlaG and in contrast to the Zn2+ ligand found in all other RNases. . ...
406 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 ...
407 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
408 5v6d 4hr2, 4ek2, 6ay1, 4dut Structure, Folding and Stability of Nucleoside Diphosphate Kinases 2020 F Georgescauld, Y Song, A Dautant- International Journal of Molecular, 2020 - mdpi.com So far, 162 structures from 30 different species have been deposited within the Protein Data Bank ( PDB ) which fall to tetramer type II and two are isolated dimers [23,24,25] (Table 1). The structure of most tetramers was recently solved by a structural genomics approach yet ... 5v6d Neisseria gonorrhoeae in complex with citrate (1.85 Å) Abendroth, J.; Mayclin, S.J.; Lorimer, D.D.; Edwards, T.E.
409 3u0i - SequenceStructureFunction Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria 2015 FH Ahmed, PD Carr, BM Lee, L Afriat-Jurnou - Journal of molecular , 2015 - Elsevier ... SequenceStructureFunction Classification of a Catalytically Diverse OxidoreductaseSuperfamily in ... Functional annotation using phylogenetic, structural, and spectroscopic methodsrevealed their ... Four novel crystal structures show that plasticity in substrate binding pockets ...
410 4f82 - The Crystal Structure of Peroxiredoxin Asp f3 Provides Mechanistic Insight into Oxidative Stress Resistance and Virulence of Aspergillus fumigatus 2016 F Hillmann, K Bagramyan, M Straburger - Scientific , 2016 - ncbi.nlm.nih.gov ... Asp f3's enzymatic activity on peroxides and structural similarity to the previously characterizedyeast-orthologue ... After failing to find a solution using the entire 4F82 model, flexible loops were ...PDB structure identifiers are 5J9B for WT Asp f3 and 5J9C for the C31S/C61S mutant. ...
411 4xxp - Placeholder factors in ribosome biogenesis: please, pave my way 2017 FJ Espinar-Marchena, R Babiano, J Cruz - Microbial Cell, 2017 - ncbi.nlm.nih.gov ... As expected from this structural similarity, cryo-EM and CRAC analyses confirmed that Tsr1 binds,albeit differently than ... MDM2 fragment was taken from 4XXP 164 after superimposing the structure shown in this file with that of L11 shown in A. ...
412 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
413 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 ...
414 3cez - Structural and biochemical analysis of mammalian methionine sulfoxide reductase B2 2011 FL Aachmann, GH Kwak, R Del Conte? - Proteins: Structure, Function, and Bioinformatics, 2011 - Wiley Online Library ... coordinate files of the minimized MsrB2 family are deposited in the Protein Data Bank (PDB) under accession ... pneumoniae (3e0o),49Neisseria meningitidis (3hcg),46Methanothermobacter thermautotrophicus (2k8d), Burkholderia pseudomallei (3cez), Neisseria gonorrhoeae ...
415 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 ...
416 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
417 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
418 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
419 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. ...
420 6c6b - Structural characterization, antifungal and cytotoxic profiles of quaternized heteropolysaccharide from Anadenanthera colubrina 2020 FOS Ribeiro, GS de Arajo, MGA Mendes- International Journal of, 2020 - Elsevier Volume 165, Part A, 15 December 2020, Pages 279-290. International Journal of Biological Macromolecules. Structural characterization, antifungal and cytotoxic profiles of quaternized heteropolysaccharide from Anadenanthera colubrina The 3D structures of all possible C. neoformans and M. canis targets were obtained from the Protein Data Bank (PDB) (Protein Data Bank, 2019) with the codes 2W3N (Carbonic anhydrase 2), 3Q73 (Farnesyl transferase), 5I33 (Adenylosuccinate synthetase), 5 U29 (Acetyl-coenzyme
421 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 ...
422 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,
423 3gbz - The N-terminal extension of UBE2E ubiquitin conjugating enzymes limits chain assembly 2013 FR Schumacher, G Wilson, CL Day - Journal of molecular biology, 2013 - Elsevier ... (a) Overlay of the core domain of UBE2E1 (3GBZ) onto the structure of UBE2D2~Ub conjugate (PDB: 3A33). The interaction between ubiquitin from one molecule, shown as a ribbon (teal) and a surface, and the backside of UBE2D2 (teal ribbon) is shown. ...
424 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 ...
425 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.. ...
426 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
427 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.
428 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
429 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). ...
430 3iml 3tde, 3s82, 3rv2 Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT from Sulfolobus solfataricus 2014 F Wang, S Singh, J Zhang, TD Huber - FEBS , 2014 - Wiley Online Library ... mjMAT Methanococcus jannaschii methionine adenosyltransferase. PDB Protein Data Bank. Pi phosphate. PPi diphosphate. ... To date, MAT structures from Escherichia coli [3, 4], Campylobacter jejuni [5], Burkholderia pseudomallei (PDB code 3IML), Entamoeba histolytica ...
431 5b8i - Wen-Luo-Tong Decoction Attenuates Paclitaxel-Induced Peripheral Neuropathy by Regulating Linoleic Acid and Glycerophospholipid Metabolism Pathways 2018 F Wu, W Xu, B Deng, S Liu, C Deng, M Wu- Frontiers in, 2018 - ncbi.nlm.nih.gov The structures of proteins were obtained from the Protein Data Bank ( PDB , https://www.rcsb.org/). Protein structures not available from PDB was homology modeled by (https://www.swissmodel. expasy.org) docking was carried out with Discovery Studio 3.5 (BIOVIA, USA) Table 6 Results of docking Proteins PDB ID pcat1 5b8i *Template of homology modeling.
432 6d8w - Molecular insights into evolution, mutations and receptor-binding specificity of influenza A and B viruses from outpatients and hospitalized patients in 2020 FX Ivan, X Zhou, SH Lau, S Rashid, JSM Teo- International Journal of, 2020 - Elsevier Structural analyses of receptor-binding specificity Then, sialotrisaccharide 3'SLN and 6'SLN isolated from co-crystallized HA-ligand structures in Protein Data Bank ( PDB ) were respectively used as the avian and human receptor analogs to assess receptor-binding
433 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).
434 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
435 3p96 - Regulatory Mechanism of Mycobacterium tuberculosis Phosphoserine Phosphatase SerB2 2017 GA Grant- Biochemistry, 2017 - ACS Publications figure Figure 1. Ribbon diagram of the structure of M. avium phosphoserine phosphatase (maPSP, Protein Data Bank entry 3p96 ) (right panel). The enzyme is a dimer with each subunit consisting of a catalytic domain (dark
436 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). ...
437 4n0w 4oh7, 4o5m, 4o5o, 4oo0, 4m0j, 4m9a Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in doubleblind predictions during the 2017 GA Khoury, J Smadbeck, CA Kieslich - Proteins: Structure, , 2017 - Wiley Online Library ... The interface will e-mail the refined structure with a unique link to visualize the initial and refinedstructures in a Jmol environment, as well as analyze the changes in key structural features whichinclude relative GDT_TS, dDFIRE energy, and number of clashes. ...
438 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
439 4k73 - Structural Basis for the Interaction and Processing of -Lactam Antibiotics by l,d-Transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis 2019 GA Libreros-Ziga, C dos Santos Silva- ACS Infectious, 2019 - ACS Publications Structural Basis for the Interaction and Processing of -Lactam Antibiotics by l,d-Transpeptidase 3 These structures revealed a fold and catalytic diad similar to those of other Ldts Mt The Ldt Mt3 faropenem structure indicated that faropenem is degraded after Cys-246 acylation The phases were obtained by molecular replacement with Phaser53 from CCP4 suite,54 adopting the PDB entries 4K73 and 5DU727 as models for LdtMt3 and LdtMt5 structures, respectively
440 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 ...
441 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
442 3khp - Proteinprotein interaction of Rv0148 with Htdy and its predicted role towards drug resistance in Mycobacterium tuberculosis 2020 G Bhargavi, S Hassan, S Balaji, SP Tripathy- BMC microbiology, 2020 - Springer Rv0148 and Htdy interaction analysis The crystallographically determined structure of Htdy ( PDB code 3KHP ) and the predicted model structure of Rv0148 were used for docking using the ClusPro server b Ramachandran plot for the predicted model structure of Rv0148
443 6tz8 - Uneditedversion published onlineon 15/7/2021 2021 G Biswas, R Banerjee - currentscience.ac.in exclusively with P2, while P1 mediates molecular recognition and binding, as evident from the crystal structures of (truncated) SurA-peptide complexes46 The crystal structure of CaEss1 showed structural similarity to the human PIN1 protein except for the
444 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 ...
445 3pm6 - Structural and Functional Characterization of Methicillin-Resistant Staphylococcus aureus's Class IIb Fructose 1, 6-Bisphosphate Aldolase 2014 GC Capodagli, SA Lee, KJ Boehm, KM Brady… - Biochemistry, 2014 - ACS Publications ... Using SaFBA along with the recent deposition of class IIb FBAs from B. anthracis (PDB Code: 3Q94) and Coccoidioides immitis (PDB Code: 3PM6) into the PDB, an updated categorization of class IIb subtypes can be envisioned (Figure 6) ...
446 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
447 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.
448 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
449 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. ...
450 4lgv - The structure of a Trypanosoma cruzi glucose6phosphate dehydrogenase reveals differences from the mammalian enzyme 2016 GF Mercaldi, A Dawson, WN Hunter - FEBS letters, 2016 - Wiley Online Library ... In M. avium and L. mesenteroides G6PDHs (PDB codes 4LGV and 1DPG respectively), thiscysteine is replaced by a valine and an alanine ... The cavity in the T. cruzi enzyme offersopportunities for a structure-based approach to develop novel G6PDH inhibitors. ...
451 5k0s - Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium 2021 GF Mercaldi, M de Oliveira Andrade- Journal of Biological, 2021 - ASBMB In addition, XcMetRS was compared with MetRS1 enzymes in complex with dual-site inhibitors from Trypanosoma brucei (PDB code: 4EGA) (48, 67), Brucella melitensis (PDB code: 5K0S) (35, 68), and S. aureus (PDB code: 4QRD)
452 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 ...
453 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
454 3cez 3cxk Structure and Electron-transfer Pathway of the Human Methionine Sulfoxide Reductase MsrB3 2020 G Javitt, Z Cao, E Resnick, R Gabizon- and Redox Signaling, 2020 - liebertpub.com MsrB3 molecules per asymmetric unit. The structure was solved by molecular replacement using a bacterial MsrB protein ( PDB code 3CEZ ) with high sequence identity to human MsrB3 (74 of 119 residues, or 62%) (6). Though the amino-terminal segment containing
455 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
456 3v7o - Viral Shapeshifters: Strange Behaviors of HIV and Other Viruses 2017 GKM Goh - 2017 - books.google.com and www.ncbi.nlm.nih.gov. Jmol and CN3D were used in this book. Sequences and structural protein databank ( PDB ) files are available at www.ncbi.nlm.nih.gov Linus Pauling discov- ered a common helical structure , the alpha helix, among pro- teins
457 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. ...
458 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
459 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
460 4dz6 - Reflections on biocatalysis involving phosphorus 2012 GM Blackburn, MW Bowler, Y Jin, JP Waltho - Biochemistry (Moscow), 2012 - Springer ... Moreo v er , kindred results can be deriv ed fro m metav ana - date co mplexes, as for the recent structure of a nucleoside diphosphate kinase with ADP linked through v anadate to His134. This show s O–P–N distance of 4.48 Å and an angle of 172.11° (PDB: 4DZ6) ...
461 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
462 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 :
463 3gka - Stereopreferences of Old Yellow Enzymes: Structure correlations and sequence patterns in enoate reductases 2011 G Oberdorfer, G Steinkellner, C Stueckler? - ChemCatChem, 2011 - Wiley Online Library ... Table 1. Protein structures used for comparison and cluster generation. Proteins, PDB accession code, Residues (Tyr/Phe/Ile) [a], Stereospecificity [b], Pseudo-atom distance [c] [?], Cluster. ... N-ethylmaleimide reductase, 3gka, Tyr?Tyr, R (ee=62 %)/S [e], 7.5, ...
464 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
465 4wbs - The structure of lipopolysaccharide transport protein B (LptB) from Burkholderia pseudomallei 2019 G Pankov, A Dawson, WN Hunter- Section F: Structural Biology, 2019 - scripts.iucr.org A single polypeptide from Paraburkholderia phymatum LptB ( PDB entry 4wbs ; Seattle Structural Genomics Center 2. The LptB subunit fold is conserved and displays no major conformational differences irrespective of whether the cofactor is present in the structure or not
466 3uam - The discovery of novel LPMO families with a new Hidden Markov model 2017 GP Voshol, E Vijgenboom - BMC Research , 2017 - bmcresnotes.biomedcentral.com ... Q3JY22. 3UAM. nd. nd. AA10 (formerly CBM33). ... The structure of one of the AA10 LPMOs fromStreptomyces coelicolor A3(2) (PDB ID: 4OY7) [39], with the copper atom shown as a sphereand highly conserved residues labeled and shown as sticks. Genome mining for LPMOs. ...
467 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 ...
468 3n5o - The Impact of Nitric Oxide Toxicity on the 2013 G Ricci, MWP Federici, PG Board, D Bovi, ML Bello… - 2013 - ASBMB ... The structural and electrostatic properties of Cys-based GSTs and Ser-based GSTs provide theexplanation for their lower affinity for DNDGIC. ... The comparison between the only availablecrystallographic structure of a DNGIC-GST complex (human GSTP1-1, PDB id: 1ZGN ...
469 3kcq - Structures and reaction mechanisms of the two related enzymes, PurN and PurU 2013 G Sampei, M Kanagawa, S Baba? - Journal of Biochemistry, 2013 - Jpn Biochemical Soc ... The structure of PurN from A. phagocytophilum HZ (PDB ID: 3KCQ) is also similar to those of PurNs described above. ... 3A and B). PurNs from M. tuberculosis (10) and A. phagocytophilum HZ (PDB ID: 3KCQ) also form the same types of dimers as AaPurN and StPurN. ...
470 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
471 5VOG - Structural analysis of (p) ppGpp reveals its versatile binding pattern for diverse types of target proteins 2020 GS Kushwaha, A Patra, NS Bhavesh- Frontiers in microbiology, 2020 - ncbi.nlm.nih.gov Although, glycosidic bond and ribose sugar in the nucleotide structure exhibit conformational flexibility and classical molecular dynamics simulation on nucleotides is S.No, Macromolecule Name, Resolution (), PDB ID 14, Putative phosphoribosyltransferase, 1.50, 5VOG
472 5eln 4efi, 3q1t Self-association of a highly charged arginine-rich cell-penetrating peptide 2017 G Tesei, M Vazdar, MR Jensen- Proceedings of the, 2017 - National Acad Sciences ionic strengths, owing to an interaction mode which is present in the structure of a MD simulations elucidate the origin of the R10R10 attraction by providing structural information on in biological systems by inspection of protein crystal structures in the Protein Data Bank ( PDB )
473 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 ...
474 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. ...
475 3p0x - Predicting Protein-Ligand Binding Sites using Support Vector Machine with Protein Properties 2013 G Wong, F Leung, S Ling - 2013 - ieeexplore.ieee.org ... The structure of proteins with bound ligands are obtained from the Protein Data Bank (PDB) [8], which ... First, the real binding sites are defined from PDB and each site is represented by a grid point in the center of it. ... They are 2cwh, 1g6c, 3p0x, 1wxg, 3kco, and 1k54. ...
476 3ej0 - Predicting protein-ligand binding site with differential evolution and support vector machine 2012 GY Wong, FHF Leung, SH Ling - 2012 International Joint Conference on Neural Networks (IJCNN), 2012 - ieeexplore.ieee.org ... Predicted quaternary structures were used rather than the tertiary structures provided in Protein Data Bank (PDB) [2]. The attributes used in SVM are selected based on the properties of protein in four different areas: ... 1AHB 1BXQ 1M5R 2ZJA 3EJ0 1C1H 1DAK 1MKA 2ZU3 3F47 ...
477 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
478 5eo6 4wsh, 4exq Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product 2017 HA Dailey, TA Dailey, S Gerdes, D Jahn… - Microbiology and …, 2017 - Am Soc Microbiol ...the structures of CgdC from yeast (PDB accession number 1TLB), human (accession number 2AEX), Leishmania major (accession number 3DWR), Leishmania donovani (accession number 3EJO), Leishmania naiffi (accession number 3E8J), and Acinetobacter baumannii (accession number 5EO6) have been solved, with all of them revealing an unprecedented fold for the monomer of large seven-stranded antiparallel β-sheets covered on both sides by α-helices..
479 3kx6 3qrh, 3mmt Molecular And 3D-Structural Characterization Of Fructose-1, 6-Bisphosphate Aldolase Derived From Metroxylon Sagu 2017 HA Roslan, M Hossain, J Gerunsin - Brazilian Archives of Biology , 2017 - SciELO Brasil ... Ten (10) proteins with highly similar structure in protein data bank ( PDB ) were identified by the COFACTOR that includes 1j4e, 1a5c, 1n30, 3kx6 , 2qdh, 3mmt ... The COFACTOR also identified msFBAld structure with the classification EC 4.1.2.13 and predicted that amino ...
480 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
481 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
482 3oks 3r4t Structures of a gamma-aminobutyrate (GABA) transaminase from the s-triazine-degrading organism Arthrobacter aurescens TC1 in complex with PLP and with its external aldimine PLP-GABA adduct 2012 H Bruce, A Nguyen Tuan? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... Acta Cryst. D66, 22-25.] ) with a monomer of the transaminase from Mycobacterium smegmatis (PDB entry 3oks ; 63% amino-acid sequence identity to A1R958; Seattle Structural Genomics Center for Infectious Disease, unpublished work) as a search model. ...
483 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 ...
484 4qq7 - Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica 2016 H Do, IS Kim, BW Jeon, CW Lee, AK Park, AR Wi - Scientific Reports, 2016 - nature.com ... C with an RMSD of 2.07 ) and the putative stringent starvation protein A from Burkholderiacenocepacia (PDB code 4QQ7) (122 aligned C ... The dimer structure of CLIC1 has a largehydrophobic surface, which can be used for membrane incorporation and chloride ion ...
485 5idv - Synthesis, spectroscopic properties, crystal structure, antimicrobial properties and Molecular Docking Studies of the complex (1) 3 (C36H24MnN6) 6 (PF6). 0.5 H2O 2018 HEL Hamdani, MEL Amane, C Duhayon- Journal of Molecular Structure, 2018 - Elsevier Docking studies was proceeded by taking the five receptors (The PDB id: 1E15(S 3BU2 (S. saprophiticus), 3GFX (klipsila pnumani), 1BY3 (E. coli) and 5IDV (acinetobacter baumannii determination of complex (1) confirmed the assignments of the structure from spectroscopic data
486 4h51 4w5k, 3meb Structural Insights into a Novel Class of Aspartate Aminotransferase from Corynebacterium glutamicum 2016 HF Son, KJ Kim - PloS one, 2016 - journals.plos.org ... A) RMSD of reported AspAT structures were analyzed. PDB code 1SPA; Escherichia coli, 7AAT; Gallus gallus (cytosolic), 2CST; Gallus gallus (mitochondrial), 3PD6; Mus musculus, 4W5K; Trypanosoma brucei, 1AJR; Sus scrofa, 3MEB; Gaiardia lamblia, 1YAA; Saccharomyces cerevisiae, 4H51; Leishmania major, 3K7Y; Plasmodium falciparum, ...
487 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
488 3tf6 - Neural networks for improving drug discovery e fficiency 2019 H Hassan Harrirou - 2019 - research-collection.ethz.ch The PDBBind 2018 general set version contains 19588 biomolecu- lar structures , for which some SMILES or FASTA), or full 3D representations of atom coordinates (ie PDB ), with bonds preferable properties of inputs to most machine-learning algorithms: a fixed-size structure
489 4pfz - Structural insights into a maleylpyruvate hydrolase from sphingobium sp. SYK-6, a bacterium degrading lignin-derived aryls 2019 H Hong, H Seo, KJ Kim- Biochemical and biophysical research, 2019 - Elsevier delta-isomerase from Mycobacterium smegmatis strain ATCC 700084 ( PDB code 4PFZ , 41% sequence The model building and structure refinement were performed as in SsMPH Apo type Mn 2+ -pyruvate have been deposited in the Protein Data Bank with PDB codes 6JVV
490 3rr6 4maq, 4pfz, 3qdf Sequence, structure and functionbased classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies 2020 H Hong, H Seo, W Park, KJ Kim- Environmental microbiology, 2020 - Wiley Online Library This article is protected by copyright. All rights reserved. Page 24. uncharacterized protein from M. abscessus DSM 44196 ( PDB code 3RR6 , 36 % sequence identity) as a search model. The structure model was built using the WinCoot program (Emsley
491 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 ...
492 4lgv - Structural basis for substrate recognition of glucose-6-phosphate dehydrogenase from Kluyveromyces lactis 2021 HH Vu, C Jin, JH Chang- Biochemical and Biophysical Research, 2021 - Elsevier The overall structure of Kluyveromyces lactis G6PD (cyan), Homo sapiens G6PD ( PDB code, 2BHL; red), Trypanosoma cruzi code, 6D23; yellow), Leuconostoc mesenteroides G6PD ( PDB code, 1DPG; purple), and Mycobacterium avium G6PD ( PDB code, 4LGV ; green)
493 3kw3 - The crystal structure of alanine racemase from Streptococcus pneumoniae, a target for structure-based drug design 2011 H Im, ML Sharpe, U Strych, M Davlieva? - BMC Microbiology, 2011 - biomedcentral.com ... of this enzyme from a further six microorganisms have been deposited in the PDB: Bartonella henselae (PDB ID 3KW3), Oenococcus oeni ... are listed in Table 1. Structure factors and final atomic coordinates for AlrSP have been deposited in the Protein Databank (PDB ID: 3S46). ...
494 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) ...
495 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
496 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
497 3oks - YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations 2018 H Land, MS Humble- Protein Engineering, 2018 - Springer File > Load > yob file from Your working directory. File > Load > Pdb file from internet. To align the structures [31] 1.531. 386 g. 29.8. 3OKS h. 1.702. 717. 27.8 g Monomer. h Crystal structure (444 residues) of a 4-aminobutyrate transaminase from Mycobacterium smegmatis [34]
498 3r1i - Structural and biochemical characterization of 20-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32 2019 HL Doden, RM Pollet, SM Mythen, Z Wawrzak- Journal of Biological, 2019 - ASBMB replacement with the structure of an SDR from Mycobacterium marinum ( PDB : 3R1I ) and refined indicate these alanine substitutions did not sig- nificantly affect secondary structural elements (Fig extended N-terminus is important for second- ary and quaternary structure In both
499 4qgr 4lc3 Templatebased modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30 2016 H Lee, M Baek, GR Lee, S Park - Proteins: Structure, , 2016 - Wiley Online Library ... The structural similarity of oligomer templates to the experimental structure of the target (releasedafter the ... T90, 0.927/2OGA, 0.927/2OGA(0.903/4LC3), 0.921/4QGR(0.915/3B8X). ... with the givendimeric state was not available in the PDB, but a dodecamer structure (PDB ID: 3RCO ...
500 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)...
501 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
502 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 ). ...
503 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
504 3tcq - Molecular docking based screening of compounds against VP40 from Ebola virus 2016 HMA El-Din, SA Loutfy, N Fathy, MH Elberry - , 2016 - bioinformation.net ... Figure 1: A 3D structure cartoon representation of the matrix protein VP40 from Ebola virus ofSudan (PDB ID: 3TCQ) as viewed in JSmol (JavaScript). (http://www.rcsb.org) mention PDB IDused; Software used: Describe the salient features of the protein in 2 statements. ...
505 4xfd - Validation of NAD synthase inhibitors for inhibiting the cell viability of Leishmania donovani: In silico and in vitro approach 2019 H Mandal, S Vijayakumar, S Yadav- Structure and, 2019 - Taylor & Francis Skip to Main Content
506 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
507 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
508 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)] ...
509 4g6c - New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs 2020 H Okella, JJ Georrge, S Ochwo, C Ndekezi- Frontiers in, 2020 - ncbi.nlm.nih.gov a global docking procedure in four folds, motif-based prediction based on peptide conformation, rigid-body docking, scoring based on structural clustering; and final structure minimization. ... The affinity of peptide-motifs A15_B and A15_E was highest within chains of the target proteins (PDB ID 1rrv, 4g6c, and 4oj8).
510 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. ...
511 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
512 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). ...
513 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
514 4ol9 4qji Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents 2020 HS Butman, TJ Kotz, CS Dowd- Frontiers in Cellular and, 2020 - ncbi.nlm.nih.gov This review gathers literature reports on the structure /mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway... To date, there is very little information available for the Mtb PanE homologue (MtPanE). The activity of the protein expressed by the putative panE gene (Rv2573) has not been experimentally verified, although its crystal structure bound to NADP+ and oxamate has been solved (PDB ID: 4OL9).
515 3qxz - Purification, crystallization and X-ray crystallographic analysis of enoyl-CoA hydratase/isomerase-family protein from Cupriavidus necator H16 2018 H Seo, KJ Kim- Biodesign, 2018 - bdjn.org The structure of H16_B0756 was determined by molecular replacement with the CCP4 version of MOLREP (Vagin and Teplyakov 2009) using the structure of probable enoyl-CoA hydratase/isomerase from Mycobacterium abscessus ( PDB code 3QXZ ) as a search model
516 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
517 3sbx 3qua Structural insight into molecular mechanism of cytokinin activating protein from Pseudomonas aeruginosa PAO1 2018 H Seo, KJ Kim- Environmental microbiology, 2018 - Wiley Online Library 29.9), Mycobacterium marinum (MmLOG, PDB code 3SBX , Z-score 28.7), Mycobacterium PDB code 5AJU, Z-score 27.2), with amino acid identities higher than 40%. In contrast, the structure of PA4923 shows relatively low homology to type-II LOGs, such as those from
518 3sbx - Structural basis for a novel type of cytokinin-activating protein 2017 H Seo, KJ Kim - Scientific Reports, 2017 - ncbi.nlm.nih.gov ... M. marinum (MmLOG) in complex with AMP (Protein Data Bank code 3SBX) revealed the ... Therefined model of CgLOGII was deposited in the Protein Data Bank (PDB code 5WQ3 ... Thethree-dimensional structure of Lonely Guy from Claviceps purpurea provides insights into the ...
519 3sbx - Structural basis for cytokinin production by LOG from Corynebacterium glutamicum 2016 H Seo, S Kim, HY Sagong, HF Son, KS Jin - Scientific , 2016 - ncbi.nlm.nih.gov ... also showed that LOGs from C. purpurea (CpLOG, PDB CODE 5AJT, Z-score 26.8) and M.marinum (MmLOG, PDB CODE 3SBX, Z-score ... To compare CgLOG with other LOGs, wesuperposed the CgLOG structure with other LOG proteins such as AtLOG3, CpLOG, and ...
520 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
521 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 ...
522 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 ...
523 3emj 3ld3, 3lo0, 3gvf, 3fq3 The Structural Basis for inorganic Pyrophosphatase Catalysis and Regulation 2011 H Tuominen - 2011 - doria.fi ... In addition, the PPase structures from five other species (Anaplasma phagocytophilum, Ehrlichia chaffeensis, Burkholderia pseudomallei, Brucella melitensis and Rickettsia prowazekii) (PDB ID: 3LD3, 3LO0, 3GVF, 3FQ3 and 3EMJ, respectively) obtained in the latest structural ...
524 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
525 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...
526 3h81 - Molecular insight into the acryloyl-CoA hydration by AcuH for acrylate detoxification in dimethylsulfoniopropionate-catabolizing bacteria 2017 HY Cao, P Wang, F Xu, PY Li, BB Xie, QL Qin- Frontiers in, 2017 - frontiersin.org Structure Determination and Refinement. The structure of RdAcuH was solved by molecular replacement using Phaser (Potterton et al., 2003). An enoyl-CoA hydratase ( PDB ID code: 3H81 ) was used as the searching model
527 6ao8 - Mutations in ArgS Arginine-tRNA Synthetase Confer Additional Antibiotic Tolerance Protection to Extended-Spectrum--Lactamase-Producing Burkholderia 2020 H Yi, J Park, KH Cho, HS Kim- Antimicrobial Agents and, 2020 - Am Soc Microbiol To investigate the ArgS function affected by the mutations, we first computationally predicted the B. thailandensis ArgS structure by using the homologous structure of Neisseria gonorrhoeae (PDB accession no. 6AO8) using Modeller
528 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
529 3qhx - Structural Insights into Substrate Specificity of Cystathionine -Synthase from Corynebacterium glutamicum 2017 HY Sagong, KJ Kim - Journal of agricultural and food chemistry, 2017 - ACS Publications ... protein mass was 2.13 3 Da 1 with a solvent content of approximately 42.27%.(17) The structure of CgMetB was determined by molecular replacement with the CCP4 version of MOLREP,(18) with the structure of MetB from M. ulcerans ( PDB code 3QHX ) used as ...
530 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,
531 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
532 5udf - Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria 2021 I Alav, J Kobylka, MS Kuth, KM Pos, M Picard- Chemical, 2021 - ACS Publications Journal Logo. Structure , Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Ilyas Alav Ilyas Alav. Institute of Microbiology and Infection, College of Medical and Dental Sciences
533 3ezl - Structure, Dynamics, and Interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 Examined by Molecular Modeling, Simulation, and Electrostatic … 2015 I Bhutani, S Loharch, P Gupta, R Madathil, R Parkesh - PloS one, 2015 - dx.plos.org ... and Lys-418 based on the active site residues of the templates (PDB ID: 4F4Q ... Another interestingobservation was high structural similarity of generated three-dimensional structure of DprE2 withSDR family members such as acetoacetyl-coA reductase (PDBID: 3EZL, rmsd: 3.43 ...
534 2mj3 - Understanding and modulating electron transfer through ferredoxins 2020 I Campbell - 2020 - scholarship.rice.edu 3.6. Cyanophage Fd structural characterization ..... 79 This bioinformatic study highlights understudied PECs whose structure , stability, and partner specificity should be further characterized... 1UWM, 1PDX, 1M2D, 1I7H, 3AH7, 2MJD, 2MJ3, 2Y5C, 5FFI, 3P1M, 1E0Z, 1DOI
535 4dz4 - Structure of the E. coli agmatinase, SPEB 2021 I Chitrakar, SF Ahmed, AT Torelli, JB French- Plos one, 2021 - journals.plos.org The first stage used the default parameters with the structure of Burkholderia thailandensis hypothetical agmatinase ( 4DZ4 ) [34] as To place the ligand in the SPEB active site, the structure of the D. radiodurans agmatinase with bound hexane-1,6-diamine ( PDB code 1WOG
536 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. ...
537 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). ...
538 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 )
539 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
540 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
541 5idv - Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization 2018 I Josts, S Niebling, Y Gao, M Levantino, H Tidow- IUCrJ, 2018 - scripts.iucr.org A total of 30 independent DAMMIF (Franke & Svergun, 2009) runs were performed to generate the initial structure pool (fit not shown). Calculated difference curves between the crystallographic dimer and monomer ( PDB codes 3b60 and 5idv ) show features similar to
542 6nb3 6vxx, 6vyb, 6nb6, 6nb4, 6nb7 Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel 2020 I Mercurio, V Tragni, F Busto, A De Grassi- Cellular and Molecular, 2020 - Springer Download PDF. Download PDF. Original Article; Published: 04 July 2020. Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies
543 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)
544 4djt - Strukturn-a sekvenn-zvisl identifikace funkn vznamnch aminokyselin v proteinov rodin. 2015 I Peclinovsk - 2015 - dspace.cuni.cz The objective is also to test P2RANK specialized tool developed at the Charles University in Prague that predict ligand binding sites from protein structure in different families 1.1 Keywords Small GTPases, Rho, Ras, Rab, Ran, Arf, PDB , Uniprot, MSA, Consurf, Sca5, P2RANK
545 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. ...
546 2khp - Staphylococcus aureus NrdH redoxin is a reductant of the class Ib ribonucleotide reductase 2010 I Rabinovitch, M Yanku, A Yeheskel? - Journal of Bacteriology, 2010 - Am Soc Microbiol ... The C. ammoniagenes NrdH X-ray structure (PDB accession number 1R7H) (39) was the best result, followed by the Brucella melitensis glutaredoxin nuclear magnetic resonance (NMR) structure (PDB accession number 2KHP) and the E. coli NrdH X-ray structure (PDB ...
547 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
548 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 ...
549 4djt - The Structure of the G Domain of the Ras Superfamily 2014 IR Vetter - Ras Superfamily Small G Proteins: Biology and …, 2014 - Springer ... series) (24 PDB files, 31 chains). ... The structure of an orthologue of Ran from Encephalitozooncuniculi (4djt, unpublished) has all GTP-interacting motifs including the catalytic glutamineconserved. It was crystallized in the GDP-bound form. ... Structure/Fold Des 15(12):1618–1629.
550 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
551 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
552 6tys - Study of Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal-X) of Monoclonal mice/human antibodies 2021 IV Ferrari, P Patrizio- bioRxiv, 2021 - biorxiv.org zone between 150-210 residues amino acids; with the exception of ID PDB 3I9G-3W9D 6TYS : (A potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits Nipah virus and Antibodies all have the same basic structure consisting of two heavy and two light
553 4f36 4fky, 4f4a, 4fkx, 4p8r The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected DiseasesPart III: In-Silico Molecular Docking 2016 IV Ogungbe, WN Setzer - Molecules, 2016 - mdpi.com ... accessibilities: (1) in most cases the protein is modeled as a rigid structure without flexibility;(2 ... compounds that may themselves function as efficacious drugs, may serve as lead structuresfor chemical modification and optimization, or provide structural templates for de ...
554 3p10 3pk0, 3p32, 3p4i Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX 2012 JA Bell, KL Ho, R Farid - Acta Crystallographica Section D: Biological Crystallography, 2012 - scripts.iucr.org ... This requirement ensured that the test set deposited in the PDB was likely to be the one that was actually used in the refinement of the deposited coordinates. ... Table 1 Characteristics of ultrahigh-resolution protein structures. `Corrected', PDB code, Resolution (?), No. ...
555 6c9e 5vpr Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases 2020 JA Dunkle, MR Bruno, PA Frantom- Section D: Structural Biology, 2020 - scripts.iucr.org Q5ZXX6 6c9e , A L. pneumophila Lpg0604 Resting state Page 7 Six sequences/ structures belong to the IPR010970 SufS family by sequence homology, and inspection of these structures reveals that five possess the -hairpin structure and one, PDB entry 5vpr from
556 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 ...
557 3he2 - THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria 2016 JAG Cox, KA Abrahams, C Alemparte - Nature , 2016 - nature.com ... Using M. tuberculosis EchA6 (PDB entry 3HE2) as a search model, we determined initial phases by molecular replacement (PHASER39). The models were rebuilt and refined (COOT40, REFMAC541, PHENIX.REFINE42) using non-crystallographic symmetry ...
558 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
559 6q05 - Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS 2020 JA Jaimes, NM Andre, JK Millet- arXiv preprint arXiv, 2020 - arxiv.org Protein Data Base: HCoV-HKU1 ( PDB # 5I08), MHV ( PDB # 3JCL), MERS-CoV ( PDB # 6Q05 ), SARS-CoV ( PDB # 5X58), FCoV-UU4 ( PDB # 6JX7), IBV-M41 ( PDB # 6CV0) and HCoV-NL63 ( PDB # 5SZS). Pairwise S structure . Additional
560 6q05 - Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein reveals an evolutionary distinct and proteolytically sensitive activation loop 2020 JA Jaimes, NM Andr, JS Chappie, JK Millet- Journal of molecular, 2020 - Elsevier Volume 432, Issue 10, 1 May 2020, Pages 3309-3325. Journal home page for Journal of Molecular Biology. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop
561 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
562 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
563 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
564 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. ...
565 5i1f - Structure of the Bacillus anthracis dTDP-l-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA) 2017 J Baumgartner, J Lee, AS Halavaty- Section F: Structural, 2017 - scripts.iucr.org The Mg2+ ion is modeled from the RffH structure The GalU homologs are from Burkholderia vietnamiensis ( PDB entry 5i1f ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Sphingomonas elodea ( PDB entry 2ux8), respectively
566 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.
567 6ws6 - Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2 2020 JB Case, PW Rothlauf, RE Chen, Z Liu, H Zhao- Cell host &, 2020 - Elsevier Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput-imaging-based neutralization assay at biosafety level 2 ... VIR antibody set Pinto et al., 2020 S309 PDB: 6WS6
568 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 ...
569 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). ...
570 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 ...
571 3i4e 3p0x Residues Asn214, Gln211, Glu219 and Gln221 contained in the subfamily 3 catalytic signature of the isocitrate lyase from Pseudomonas aeruginosa are involved in its catalytic and thermal properties 2013 J Campos-Garcia, C Diaz-Perez? - World Journal of Microbiology and Biotechnology, 2013 - Springer ... The ICL-Pa model in the open state was built using homologous ICL from A. nidulans (PDB 1DQU), Burkholderia pseudomallei (PDB 3I4E), and E. coli (PDB 1IGW), whereas the closed state model was built using the closed model of a homologous ICL from Brucella melitensis ...
572 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
573 4mei 4kz1, 4nhf, 4lso, 4jf8, 4o3v Structural and Biochemical Analysis of OrfG: The VirB8-like Component of the Conjugative Type IV Secretion System of ICESt3 From Streptococcus 2021 J Cappele, A Mohamad Ali- Frontiers in molecular, 2021 - frontiersin.org The first step of structure comparison was conducted with both DALI (Holm and Sander, 1995) and and Henrick, 2004) to fetch a complete list of VirB8 structures (26 PDB entries 16 structures was conserved (2cc3, 3ub1, 3wz3, 3wz4, 4akz, 4ec6, 4jf8, 4kz1, 4lso, 4mei , 4nhf, 4o3v
574 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
575 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. ...
576 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),
577 6nb6 - Review of COVID-19 antibody therapies 2021 J Chen, K Gao, R Wang, DD Nguyen- Annual review of, 2021 - annualreviews.org S230 SARS-CoV RBD IgG = 0.06 / BLI (73) 6NB6 (73) 4.30 Three-Dimensional Structure Alignment All of the available 3D structures of the SARS-CoV-2 S-protein RBD in complex with antibod- ies are aligned to ACE2 The PDB ID of these complexes can be found in Table 1
578 6wps 7jvc, 7jva, 7jv6, 7jx3, 7k45, 7jw0 Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies 2021 J Chen, K Gao, R Wang, GW Wei- Chemical science, 2021 - pubs.rsc.org Our predictions are built from the X-ray crystal structure of SARS-CoV-2 S protein and ACE2 ( PDB 6M0J), 57 and various antibodies (PDBs 6WPS , 66 6XC2, 58 6XC3, 58 6XC4, 58 6XC7, 58 6XE1, 64 6XEY, 83 6XKP, 72 6XKQ, 72.
579 5elo 6aqg, 5vl1, 6c86 Side chain rotameric changes and backbone dynamics enable specific cladosporin binding in Plasmodium falciparum lysyltRNA synthetase 2019 J ChhibberGoel, A Sharma- Proteins: Structure, Function, and, 2019 - Wiley Online Library ( PDB : apo 6C86, holo 5ELO ) and M. ulcerans (MuKRS) ( PDB : apo 5VL1, holo re-arrangements and are noted as 1 to 4 for all the four PDB data sets (Table 1 and Fig. 1). In based on structural analyses. Our analyses also provide a platform for structure -guided
580 3gp5 4dz6, 3gw8 Vanadium and proteins: Uptake, transport, structure, activity and function 2015 JC Pessoa, E Garribba, MFA Santos… - Coordination Chemistry …, 2015 - Elsevier ...A more recent 2.2 Å structure of a transition state nucleoside diphosphate kinase from Borrelia burgdorferi bound to vanadate(V) and ADP was deposited (PDB: 4DZ6) ... Later the structure of the bacterial dPGM from Burkholderia pseudomallia was also solved complexed with vanadate(V) (PDB: 3GW8 and 3GP5) [319]; in the 3GW8 structure at 1.9 Å resolution, glycerol, from the crystallization conditions, reacted with vanadate(V) forming a species quite similar to the enzymatic substrate. ...
581 3ej2 - Synthesis and Activity of 1, 2, 3-Triazolyl-chalcones Against the Fungus Colletotrichum lindemuthianum 2018 JC Pessoa, RF Azevedo, SF Mota- Letters in Organic, 2018 - ingentaconnect.com 3.6. Enzymes Complexed with Ligands Similar to Com- pound 1a The structure of compound 1a proteins were downloaded from the RCSB Protein Data Bank (http://www. pdb .org) [36 protein kinase (STPK; code: 2AYP) [29], inorganic phosphatase (IP; code: 3EJ2 ) [30], Bruton's
582 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
583 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
584 3mmt - Uniquely Localized Intra-Molecular Amino Acid Concentrations at the Glycolytic Enzyme Catalytic/Active Centers of Archaea, Bacteria and Eukaryota are Associated with Their Proposed Temporal Appearances on Earth 2013 JD Pollack, D Gerard, DK Pearl - Origins of Life and Evolution of Biospheres, 2013 - Springer ... We thank A. S. Gardberg, Emerald BioStructures, Seattle, WA for advice concerning the composition of the C/AC of PDB 3mmt FBPA of Bartonella henselae. ...
585 6mg6 - Nitrilase: a promising biocatalyst in industrial applications for green chemistry 2021 JD Shen, X Cai, ZQ Liu, YG Zheng- Critical Reviews in, 2021 - Taylor & Francis 6I00), Saccharomyces cerevisiae ( PDB : 4H5U and 1F89), Pyrococcus abyssi ( PDB : 3KLC), Helicobacter pylori ( PDB : 6MG6 ) and Synechocystis ( PDB : 3WUY) has been obtained However, with most of the nitrilases, the crystal structure had been resolved, came from eukaryotes
586 4kzk - Structural Flexibility of Peripheral Loops and Extended C-Term Domain of Short Length Substrate Binding Protein from Rhodothermus marinus 2019 JE Bae, IJ Kim, Y Xu, KH Nam - 2019 - preprints.org 120 analysis and substrate docking studies using previously reported crystal structure of SBP ( PDB 121 code 5Z6V) as starting point model structure Among them, 9 models ( PDB code: 123 2QH8, 3LFT, 5ER3, 6DSP, 5BRA, 3KSM, 2DRI, 5DTE, 4KZK , 4RS3, 8ABP) with
587 4kzk - Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus 2021 JE Bae, IJ Kim, Y Xu, KH Nam- The protein journal, 2021 - Springer of RmSBP, we performed comparative analysis and substrate docking studies using a previously reported crystal structure of SBP ( PDB code 5Z6V) as the initial model structure Among them, 9 models ( PDB codes: 3LFT, 2QH8, 5ER3, 4RS3, 4KZK , 5BRA, 3KSM, 2DRI
588 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 ...
589 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% ...
590 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
591 6q06 - Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection 2020 J Fantini, C Di Scala, H Chahinian, N Yahi- International journal of, 2020 - Elsevier N-acetylneuraminic acid (Neu5Ac) was generated with the Hyperchem database. 9-O-acetyl-N-acetylneuraminic acid (9-O-SIA) was retrieved from pdb file 6Q06 [18] Its three-dimensioanl structure was retrieved from pdb file # 4V2O [19]
592 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 ...
593 3ke1 - Thiazolopyrimidine Inhibitors of 2‐Methylerythritol 2, 4‐Cyclodiphosphate Synthase (IspF) from Mycobacterium tuberculosis and Plasmodium falciparum 2010 JG Geist, S Lauw, V Illarionova, B Illarionov, et al. ChemMedChem (2010) 5:1092-1101 ...[11] T.E. Edwards, D.R. Davies, R. Hartley, W. Zeller, unpublished results. PDB code: 3KE1....
594 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. ...
595 4k9d - Surface-displayed glyceraldehyde 3-phosphate dehydrogenase and galectin from Dirofilaria immitis enhance the activation of the fibrinolytic system of the host 2015 J González-Miguel, R Morchón, M Siles-Lucas… - Acta tropica, 2015 - Elsevier ... msa/clustalw2/) and prediction of the secondary structures and three-dimensional modeling with the Swiss-Model server ( Arnold et al., 2006; http://swissmodel.expasy.org/) using as templates the X-ray crystal structure of a GAPDH from B. malayi (code pdb: 4K9D) for DiGAPDH ...
596 3sbx - Structures of the calcium-activated, non-selective cation channel TRPM4 2017 J Guo, J She, W Zeng, Q Chen, X Bai, Y Jiang- Nature, 2017 - nature.com cytosolic region of about 700 amino acid residues with uncharacterized structure and function particle electron cryo-microscopy (cryo-EM), revealing the unique molecular architecture of the Along with electrophysiological analysis, we also elucidated the structural basis of ATP ... structural comparison between the NBD of ATP-bound TRPM4 and AMP-bound LOG protein (PDB accession number 3SBX).
597 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. ...
598 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. ...
599 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) ...
600 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. ...
601 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 ...
602 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
603 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
604 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 ...
605 5j92 - Preferential catabolism of the (S)enantiomer of the herbicide napropamide mediated by the enantioselective amidohydrolase SnaH and the dioxygenase Snpd in 2019 J Huang, D Chen, J Jiang- Environmental microbiology, 2019 - Wiley Online Library molecular docking. A homology model of Snpd was built based on chain A of the 5J92 template (sharing 39% identity with Snpd; PDB code; resolution: 1.95 ). A Snpd- KG-FeO complex structure was established in a similar manner as SnaH-Zn-H2O. The
606 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
607 3h81 - Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase 2020 J Hwang, CS Jeong, CW Lee, SC Shin, HW Kim- Journal of, 2020 - Springer (D) The electrostatic surface potential of the trimeric HyECH structure also shows that the periphery of the putative ligand-binding site has a positive charge MtECH, ECH from M. tuberculosis ( PDB code 3H81 ). Page 7. Crystal structures of BoECI and HyECH 7
608 4h3e - The Crystal Structure of the Manganese Superoxide Dismutase from Geobacillus stearothermophilus: Parker and Blake (1988) Revisited 2020 JJ Adams, CJ Morton, MW Parker- Australian Journal of Chemistry, 2020 - CSIRO determined primarily by X-ray crystallography, although one SOD structure has been SODs have also been determined from Pseudomonas putida (ovalis) ( PDB ID: 1dto acidocaldarius (1b06), [ 27 ] Acanthamoeba castellanii (6j55), [ 28 ] Trypanosoma cruzi ( 4h3e ), [ 29 ] Vigna
609 4nbr - MRREX: molecular replacement by cooperative conformational search and occupancy optimization on lowaccuracy protein models 2018 JJ Virtanen, Y Zhang- Acta Crystallographica Section D, 2018 - Wiley Online Library et al., 2016, 2017; Shrestha & Zhang, 2015), MR-REX takes advan- tage of this fact by predicting possible inaccurate segments of the structural model and Input and output data The input to MR-REX is a set consisting of structure -factor data, a structure file in PDB format and
610 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 )
611 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 ?. ...
612 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
613 3uw1 - Understanding the interaction of antibodies and transcription factors with their ligands through structural biology 2015 J kerlov - 2015 - dspace.cuni.cz One such enzyme, ribose-5-phosphate isomerase A from Burkholderia thailandensis (PDB code 3UW1 [157]) also binds its substrate ribose-5-phospate in a linear form in an orientation very similar to that of deoxyribose-5-phosphate in C-DeoR
614 6q06 - Molecular diversity of coronavirus host cell entry receptors 2020 JK Millet, JA Jaimes, GR Whittaker- FEMS microbiology reviews, 2020 - academic.oup.com boxes indicate genes encoding accessory proteins (ns2, ns4a, ns4b and ns5a), while green boxes indicate structural proteins B) Representative structure of coronavirus protein in pre-fusion (S1 and S2 subunits, PDB 3JCL) and post-fusion (S2 subunit, PDB 6B3O) conformations ...MERS-CoV NTD (PDB 6Q06), which binds sialosides with a preference for α2,3-linked sialic acids,
615 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
616 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
617 4iv5 - Theory, Design and Characterization of Protein Symmetry Combination Materials 2020 J Laniado - 2020 - search.proquest.com The symmetry group of a structure can be used to understand how many structurally distinct contact types are required to hold all the Current Opinion in Structural Biology 2016, 39:134143 built into a protein building block in order for it to assemble into the desired architecture
618 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
619 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
620 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 ...
621 6pqh - Structural study of the N-terminal domain of human MCM8/9 complex 2021 J Li, D Yu, L Liu, H Liang, Q Ouyang, Y Liu- Structure, 2021 - Elsevier Journal home page for Structure . Article. Structural study of the N-terminal domain of human MCM8/9 complex Show more Share. Cite Highlights. The heterohexameric NTD structure combined crystal structures with cryo-EM map. ...Some other structures with less than 2.0 Å RMSD include DNA-directed DNA polymerase III (PDB: 3F2B), asparagine-tRNA ligase (PDB: 6PQH), replication protein A (PDB: 2K5V), telomerase-associated protein
622 4lfy - Pyrimidine biosynthesis in pathogensStructures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae 2019 J Lipowska, CD Miks, K Kwon, L Shuvalova- International journal of, 2019 - Elsevier As the first DHO structure ( PDB ID 1J79) was deposited in 2001, structural information was not available to guide the DHO classification proposed in 1999. In 2014, an updated phylogenetic tree based on structure -guided sequence alignments using structures available for nine .. Table 1 Burkholderia cenocepacia 4LFY 2013 Structural genomics (SSGCID)
623 4kyx - Structural insights into the substrate recognition mechanism of Arabidopsis thaliana GPP-bound NUDX1 for noncanonical monoterpene biosynthesis 2017 J Liu, Z Guan, H Liu, L Qi, D Zhang, T Zou, P Yin- Molecular Plant, 2017 - Elsevier ... P2 2121, determined 52 the structure by molecular replacement based on the available coordinates (MutT, PDB : 53 4KYX ) and refined ... Furthermore, our findings provide new opportunities for structure -guided 156 enzyme engineering (Wurtzel and Kutchan, 2016) and the ...
624 4kyx - Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis 2018 J Liu, Z Guan, H Liu, L Qi, D Zhang, T Zou, P Yin- Molecular plant, 2018 - cell.com the structure by molecular replacement based on the available coordinates (MutT, PDB : 53 4KYX ) and refined the structure at a resolution of 1.39 (Supplemental Table 1). Most of 54 such as FPP. Furthermore, our findings provide new opportunities for structure -guided 156
625 3lr0 - The role of hydrophobic interactions in folding of -sheets 2020 J Li, X Ma, H Zhang, C Hou, L Shi, S Guo- arXiv preprint arXiv, 2020 - arxiv.org Nature Structural Biology 10, 980, doi:10.1038/nsb1203-980 (2003). 19 Berman, H., Henrick, K., Nakamura, H. & Markley, JL The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data Structure relaxation via long trajectories made stable
626 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 ...
627 5i3e - Targeting Protein-Protein Interactions for Disruption of LSD1 (KDM1A) Complexes 2017 JL Schwabe - 2017 - dukespace.lib.duke.edu (b) A predicted structural model generated used to determine sites of protein-protein interactions, which can be illustrated, for example, on available crystal structures in the CoREST samples were mapped onto an available LSD1/CoREST co-crystal structure ( PDB 2IW5) as a
628 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)
629 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
630 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)
631 5ifz - SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for 2018 JM Dana, A Gutmanas, N Tyagi, G Qi- Nucleic acids, 2018 - academic.oup.com 5.3.1.34 D-erythrulose 4-phosphate isomerase Q9ZB26 99% 5ifz 5.3.1.6 Ribose-5 of the protein sequence space 40-fold, expanding the applicability of structure -based an positions from Ensembl enables a more direct cross-referencing of genomic data from PDB structures
632 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 ...
633 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
634 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
635 3mc4 - The cysteine regulatory complex from plants and microbes: what was old is new again 2013 JM Jez, S Dey - Current opinion in structural biology, 2013 - Elsevier ... To date, both hexameric and trimeric SAT have been described in the literature [ 12?, 13, 14 and 15 ] and as unpublished structures (PDB: 3GVD, 3MC4, 3F1X). The hexameric SAT are a dimer of trimers associated through a head-to-head orientation of the N-terminal domains. ...
636 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
637 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)
638 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
639 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 ...
640 6tys - Planejamento de protenas imunognicas multi-eptopo visando o desenvolvimento de uma vacina de nova gerao para a infeco do vrus Nipah 2020 JMP GALCIO - 2020 - repositorio.ufopa.edu.br -defensin adjuvants were also added to the structural models to increase immunogenicity The interactions between each predicted epitope and MHC-I and MHC- II structures were also analyzed, using molecular modeling P Fosfoprotena PDB Protein Data Bank
641 3v7n - Regulation of Neural Progenitor Cell and Glioma Stem Cell Proliferation by Id2 and Hey1 2016 JM Sullivan - 2016 - search.proquest.com The Swiss-model webserver (http://swissmodel.expasy.org/interactive#structure) was used to generate homology models of the terminal regions (residues 6-57 and 63-115) of WT ID2 using the “Upload-Template” protocol [195]. PDB id: 1MH2 and PDB id: 3V7N were the proteins with the highest similarity for the N-terminus and C-terminus of Id2 respectively.
642 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
643 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).
644 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.
645 4odj - Structure of a critical metabolic enzyme: S-adenosylmethionine synthetase from Cryptosporidium parvum 2019 J Ohren, GF Parungao, RE Viola- Section F: Structural Biology, 2019 - scripts.iucr.org Vagin & Teplyakov, 2010) with the structure of C. hominus MetK ( PDB entry 4odj ) as the ordered in the presence of substrates, is disordered and was not modeled in this structure to form functional tetramers with D2 or 222 symmetry, as illustrated by EcoMetK ( PDB entry 1p7l
646 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 ...
647 5ids - Mrub_2052, Mrub_0628, and Mrub_2034 genes are predicted to be orthologous to b0688, b2039, and b3789 genes found in Escherichia coli, which are involved in 2017 JP Hartnett, D Scott - 2017 - digitalcommons.augustana.edu (Finn et al.). Protein Data Bank ( PDB ) (Berman et. al., 2000) is a curated collection of crystalized proteins.If a PDB hit is obtained for a query sequence, then 3-D structure neighbors, Page 7. 6 PDB protein database 5IDS Glucose-1-phosphate Thymidylyltransferase
648 5ids - Mrub_2052, Mrub_0628, and Mrub_2034 genes are predicted to be orthologous to b0688, b2039, and b3789 genes found in Escherichia coli, which are involved in 2017 JP Hartnett, D Scott - 2017 - digitalcommons.augustana.edu ... (Finn et al.). Protein Data Bank ( PDB ) (Berman et. al., 2000) is a curated collection of crystalized proteins.If a PDB hit is obtained for a query sequence, then 3-D structure neighbors, Page 7. 6 ... PDB protein database 5IDS Glucose-1-phosphate Thymidylyltransferase ...
649 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
650 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
651 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 ...
652 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
653 4odj - Redox regulation of Plasmodium falciparum methionine adenosyltransferase and Mycetinis scorodonius DyP-type peroxidase 1 2016 J Pretzel - 2016 - geb.uni-giessen.de ... Since the crystal structure of PfalMAT is not yet available, we constructed a homology model based on the crystal structures of MAT from different organisms, the alpha subunit of human MAT isoform 2 (hMAT2A) (PDB ID 2p02) and C. hominis MAT (PDB ID 4odj) ...
654 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). ...
655 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...
656 4djt - PatchSearch: a web server for off-target protein identification 2019 J Rey, I Rasolohery, P Tuffry, F Guyon- Nucleic acids, 2019 - academic.oup.com 4djt 22.3 0.376 positive 10.378 The patch was extracted around ADP in the 1lkx myosin structure . Structural similarities between the patch and the entire surface of 40 PDB structures known to be able to interact, ie 'positive', or not, 'negative', with ADP or similar ligands
657 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
658 3r4t 4ffc QSAR and Molecular Docking Studies of the Inhibitory Activity of Novel Heterocyclic GABA Analogues over GABA-AT 2018 J Rodrguez-Lozada, E Tovar-Gudio- Molecules, 2018 - mdpi.com We have previously reported the synthesis, in vitro and in silico activities of new GABA analogues as inhibitors of the GABA-AT enzyme from Pseudomonas fluorescens... To incorporate the prosthetic group (PLP) in the homology models an alignment employing a crystal structure that possessed the PLP was done (3r4t and 1ohw for the Pseudomonas and human models respectively).
659 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
660 4dyw 3hhj The evolution of function within the Nudix homology clan 2017 JR Srouji, A Xu, A Park, JF Kirsch- Proteins: Structure,, 2017 - Wiley Online Library ... Despite the structural similarity, sequence identity within the Nudix homology domain between these ... and X is any amino acid) constitutes a loop-helix-loop structure that is ... diphosphate isomerase family (represented by E. coli isopentenyl diphosphate isomerase PDB ID: 1NFS ...
661 4ffc - Polyamines in fungi 2016 J Ruiz-Herrera - 2016 - 5.63.15.51 ... come from such different sources and have in common only their chemical similarities: Polyaminealiphatic molecules (see their structures in Figure ... Figure 3.15 structure of a 4-aminobutyrate aminotransferase (GabT) from Mycobacterium abscessus, 4FFC (Baugh, l., Phan, i., Begley, D.W., Clifton, m.c., Armour ...
662 5ig2 3tjr Structural Genomics of Infectious Agents 2021 JS Alenazi - 2021 - search.proquest.com 4 1.3.5 Deposition of Structure in PDB ..... 4 identity to SDR from B.phymatum ( 5ig2 ) .... 45 S.3.2 Targeted approach of structure genomics can be applied to select the biologically important proteins
663 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 ...
664 3ek2 - Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (ACP) Reductase Inhibitor 2014 J Schiebel, A Chang, S Shah, Y Lu, L Liu, P Pan - Journal of Biological Chemistry, 2014 - ASBMB ... Molecular replacement was performed in Phaser using the PDB entry 3EK2 as a template. ... The structure factors and coordinates of the different FabI structures have been deposited in the ProteinData Bank with the PDB entry codes 4CUZ (saFabI-NADPH-PT173), 4CV1 ...
665 3iml - Structural and functional characterisation of the methionine adenosyltransferase from Thermococcus kodakarensis 2013 J Schlesier, J Siegrist, S Gerhardt, A Erb? - BMC Structural Biology, 2013 - biomedcentral.com ... for archaeal MATs. The only exception from this observation is the structure of the Burkholderia pseudomallei MAT (PDB-ID 3IML), with a less pronounced torsion of only 35?. Figure 7 Spatial arrangement of MAT monomers. ...
666 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
667 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
668 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. ...
669 3uw1 - Structure of the effector‐binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis 2014 J Škerlová, M Fábry, M Hubálek, Z Otwinowski… - FEBS …, 2014 - Wiley Online Library ... Superposition of the CggR structure with the C-DeoR structures provides RMSD values of 2.6and 2.7 Å for effector-bound and free ... view in (A). (C) Superposition of C-DeoR (green) withribose-5-phosphate isomerase A from B. thailandensis (gold, PDB code 3UW1) [11] in ...
670 3tde 3rv2, 3s82 Synthesis of non-natural cofactor analogs of S-adenosyl-L-methionine using methionine adenosyltransferase 2018 J Thorson, T Huber, J Zhang, S Singh- US Patent 9,879,043, 2018 - freepatentsonline.com marinum ( PDB code 3RV2), Mycobacterium avium ( PDB code 3S82), Mycobacterium tuberculosis ( PDB code 3TDE ), Rattus norvegicus [36 Protein Data Bank ( PDB ) ID:1RG9), hMAT2A ( PDB ID:2PO2) and hMAT1A ( PDB ID:2OBV) on the hMAT2A homodimeric structure
671 4jgb 4jga Targeting Transforming Growth Factor Beta-Activated Kinase 1 as a Therapeutic 2017 J Totzke - 2017 - dukespace.lib.duke.edu 50 3.4 Structural and functional similarities between TAK1 and related kinases ..... 50 Page 8. viii 4 Figure 2: Crystal structure TAK1 ( PDB 5V5N, left ribbon, right hydrophobicity surface) .... 11
672 4jgb 4jga TAK1: a potent tumour necrosis factor inhibitor for the treatment of inflammatory diseases 2020 J Totzke, SA Scarneo, KW Yang- Open, 2020 - royalsocietypublishing.org A general core structure for type II binders has been developed, consisting of a hydrophobic moiety Structural disorder of this region is often cited as a reason for the missing residues of Ligand 10 (purple, PDB 4JGA), 11 (orange, PDB 4JGB ) and 12 (dark green, PDB 4JGD) are
673 4iwh - Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data 2019 JT Seffernick, SR Harvey, VH Wysocki- ACS Central, 2019 - ACS Publications from which data have been favorably compared to known crystal structures on many along with other bioanalytical MS and dissociation techniques, yields useful structural information, the sparse, not allowing for an unambiguous determination of the protein complex structure... Additionally, the Pnear also improved for 56/57 ideal cases (except 4IWH) when SID data were used, as shown in Figure S3A.
674 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.
675 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 ...
676 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
677 4h51 - Structural basis for the relaxed substrate selectivity of Leishmania mexicana broad specificity aminotransferase 2015 J Wen, C Nowicki, W Blankenfeldt - Molecular and biochemical , 2015 - Elsevier ... The most similar structure, however, is that of a putative aspartate aminotransferasefrom Leishmania major Friedlin (LmajASAT, PDB entry 4H51 [16]), which was notavailable when we first determined the structure of LmexBSAT. ...
678 3qxz 3qre, 3qk8, 3swx, 4qtp, 3oc7 Similarity/dissimilarity analysis of protein structures based on Markov random fields 2018 J Wu, T Zhou, J Tao, Y Hai, F Ye, X Liu, Q Dai- Computational biology and, 2018 - Elsevier Recently, the growth of the Protein Data Bank ( PDB ) (Berman et al., 2000) has been accelerated by a large scale As a result, fast and efficient algorithms for protein structure comparison have become more important to take advantage of the huge amount of structural data
679 4qhq - The I-TASSER Suite: protein structure and function prediction 2015 J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang - Nature methods, 2015 - nature.com ... binding protein from Burkholderia cenocepacia bound to methionine (CAMEO: C0081; PDB:4qhqA) (e ... bound to calcium ion and thymidine-3′,5′-diphosphate (CAMEO: C0046; PDB:4qf4A ... on the significance of threading alignments and the density of structure clustering; the ...
680 3pfd - Site-directed mutation to improve the enzymatic activity of 5-carboxy-2-pentenoyl-CoA reductase for enhancing adipic acid biosynthesis 2019 J Yang, Y Lu, Y Zhao, Z Bai, Z Ma, Y Deng- Enzyme and Microbial, 2019 - Elsevier 3PFD was the PDB ID of the template. Therefore, we used 3PFD as the template to build the homology model of Tfu_1647 protein using DS 2017R2 [17] We then used the Deriding-like force field in DS 2017R2 to optimize the structure to ensure that we produced a
681 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
682 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
683 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
684 5i4m - Zn2+-dependent enhancement of Atrazine biodegradation by Klebsiella variicola FH-1 2021 J Zhang, X Wu, X Zhang, H Pan, JES Shearer- Journal of Hazardous, 2021 - Elsevier chloromuconate to generate maleylacetate (Cmara et al., 2008). As a major structural component in the cell wall, peptidoglycan plays important roles in cell growth. Studies have shown that three zinc-dependent endopeptidases
685 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 ...
686 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
687 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) ...
688 3nfw - The oxygen reduction reaction catalyzed by Synechocystis sp. PCC 6803 flavodiiron proteins 2019 KA Brown, Z Guo, M Tokmina-Lukaszewska- Sustainable Energy &, 2019 - pubs.rsc.org 3, 12 and 13) and provide more insights into the Flv structure , substrate reactivity and protein based on heuristics to maximize confidence, percentage identity and alignment coverage ( PDB IDs: 1VME for the oxidoreductase domain: 5ZC2, 55 3RH7, 4HX6, 56 3K87, 57 3NFW 58
689 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
690 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
691 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. ...
692 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
693 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
694 6uk3 3glq, 3n58, 3d64, 6aph, 5v96 S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains 2020 K Brzezinski- Biomolecules, 2020 - mdpi.com major [3G1U, unpublished], Cryptosporidium parvum [5HM8 unpublished], Acanthamoeba castellanii [ 6UK3 , unpublished], Naegleria Crystal structures of SAHases were acquired from PDB cofactor-binding domains was performed based on secondary structure assignments in
695 3glq 3n58 S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive formBiochemical and structural 2017 K Brzezinski, J Czyrko, J Sliwiak - International Journal of , 2017 - Elsevier ... tuberculosis [10], Bradyrhizobium elkanii [11], Burkholderia pseudomallei ( PDB entry 3GLQ ; unpublished), Brucella ... Recently, the first crystal structure of SAHase from the hyperthermophilic Thermotoga maritima ... active form has been determined and deposited in the PDB in the ...
696 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). ...
697 4h3e - Parallel Molecular Evolution of Catalases and Superoxide DismutasesFocus on Thermophilic Fungal Genomes 2020 K Chovanov, M Bhmer, A Poljovka, J Budi- Antioxidants, 2020 - mdpi.com and heme catalases were obtained from Phyre-2 server [16] by employing the intensive mode with HMM and PSI-Blast for finding closest homologs with a known experimental structure . Obtained structural models were superimposed on experimental 3D structures using the
698 3u03 - Overcoming antibiotic resistance: Is siderophore Trojan horse conjugation an answer to evolving resistance in microbial pathogens? 2017 K Dhusia, A Bajpai, PW Ramteke- Journal of Controlled Release, 2017 - Elsevier Comparative study of siderophore biosynthesis pathway in pathogens provides potential targets for antibiotics and host drug delivery as a part of computationall.
699 3cez - Understanding the Molecular Dynamics of YPEL3 and FHIT Gene Expression 2010 KD KELLEY - 2010 - etd.ohiolink.edu ... protein structure may also aid in understanding the molecular events involved in theinduction and maintenance of premature senescence. Identifying structural homologybetween a predicted model of YPEL3 and other known structures may ...
700 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 ...
701 4hvt - Pyrococcus furiosus Prolyl Oligopeptidase: A Dynamic Supramolecular Host for Peptidase and Dirhodium Catalysis 2018 K Ellis-Guardiola, H Rui, R Beckner, P Srivastava - 2018 - chemrxiv.org both Pfu POP and the S447C mutant possess a two-domain architecture involving a peptidase domain reported homology model; M. xanthus chain A from 2BKL; R. typhi from 4HVT ; S. Scrofa from 1QFS; H. Page 17 S1). The structure of
702 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
703 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
704 6nb7 - Molecular Modelling and Docking Experiments Examining the Interaction between SARS-CoV-2 Spike Glycoprotein and Neuronal Nicotinic Acetylcholine Receptors 2020 K Farsalinos, E Eliopoulos, D Leonidas - 2020 - preprints.org receptor ( PDB id: 6NB7 ) and the extracellular domain of the nAChR alpha9 subunit in complex with alpha-bungarotoxin ( PDB id: 3U8M) were downloaded from the Protein Data solved yet, we used the crystal structure of the extracellular domain of the homologous
705 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
706 4e98 - Sensory properties of the PII signalling protein family 2015 K Forchhammer, J Lddecke - FEBS Journal, 2015 - Wiley Online Library ... In the group of P II -like proteins, the HisG proteins are special because they show P II -likestructures, which are domains of larger proteins. Name, PDB code, Organism, % Seqence Identity,% Structure Similarity, Proteins in cluster. ... CutA1, 4E98, Cryptosporidium parvum, 13, 92, ...
707 3oxk - Response to Errors in Crystal structure of HINT from Helicobacter pylori 2016 KF Tarique, S Devi, SA Abdul Rehman - Section F: Structural , 2016 - scripts.iucr.org ... The confusion arises again from the various PDB entries where the same protein was namedas ... branch of the HIT family (http:// www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv ... has also beenidentified to contain purine nucleoside- and nucleotide- binding proteins' (3oxk; Lorimer et al ...
708 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.
709 5vir 4ymi, 4fry Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target 2020 KH Burley, BJ Cuthbert, P Basu- ACS Infectious, 2020 - ACS Publications \ Interestingly, the three top-scoring NADP+ molecules are found in structures of Mtb nicotinamide-mononucleotide adenylyltransferase (NadD) (PDB ID: 4S1O) and Mycobacterium abscessus NadD (PDB ID: 4YMI and 5VIR). These results
710 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
711 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
712 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]. ...
713 4z9n - Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis 2018 K Keidel, F Amman, I Bibova, J Drzmisek, V Benes- RNA, 2018 - rnajournal.cshlp.org Besides its role in the stabilization of the RNA duplexes, Hfq can also actively remodel the structure of RNAs and increase or decrease the stability of BLAST search unveiled that the BP3831 protein exhibits high homology with the entry 4Z9N in the PDB protein database
714 3swt - Virus-associated organosulfur metabolism in human and environmental systems 2021 K Kieft, AM Breister, P Huss, AM Linz, E Zanetakos- bioRxiv, 2021 - biorxiv.org oxygen binding (eg WH and H) (Knauer 198 et al., 2012). Conserved amino acid residues that are not functional are likely preserved for 199 structural features. The retention of AMGs on viral genomes despite strong selective ... Annotations of functional amino acid residues were labeled according to the Protein Data Bank (PDB, accessed January 2019) (Berman et al., 2000) with the following identification numbers: 4BZQ and 4BZP (CysC), 2GOY (CysH), 3ZEI (CysK), 3SWT (TauD), and 1RG9 (MetK).
715 3uam - Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars 2017 KK Meier, SM Jones, T Kaper, H Hansson- Chemical, 2017 - ACS Publications Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide ... Table 4. AA10 LPMO Structures Available in the Protein Data Bank Burkholderia pseudomallei LPMO10A, BpAA10A 3UAM
716 3emk - The Crystal Structure of l-Sorbose Reductase from< i> Gluconobacter frateurii</i> Complexed with NADPH and l-Sorbose 2011 K Kubota, K Nagata, M Okai, K Miyazono? - Journal of molecular Biology, 2011 - Elsevier ... Appendix A. ... Strictly conserved residues among the proteins are shown with a red background. Protein names are shown as PDB accession numbers: 2HQ1, glucose/ribitol dehydrogenase from Clostridium thermocellum; 3EMK, glucose/ribitol dehydrogenase from Brucella melitensis; ...
717 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
718 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
719 4wbs - Structural modeling of the Treponema pallidum OMPeome: a roadmap for deconvolution of syphilis pathogenesis and development of a syphilis vaccine 2021 KL Hawley, JM Montezuma-Rusca- Journal of, 2021 - Am Soc Microbiol TP0786 Phyre2 LptB; Burkholderia phymatum; 4WBS 50 conserved in T. pallidum BamA, we performed structure -based sequence alignment of the 170 TP0326 3D model with the crystal structures of E. coli BamA ( PDB ID: 5D0Q, 5D0O) (60). The 171
720 3pme - The binding of β-d-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: A new class of inhibitors 2010 KM Alexacou, AC Tenchiu, ED Chrysina… - Bioorganic & medicinal …, 2010 - Elsevier ... 11. The structural results show that all inhibitors are bound with essentially no disturbance ofthe overall protein structure. ... However, upon binding to the catalytic site compounds 3pBr, 3pCl,3pCF3, 3oOH, 3pOMe and 3pMe trigger a significant shift of the 280s loop with ...
721 6nb8 - Use of Isoelectric Point for Fast Identification of Anti-SARS CoV-2 Coronavirus Proteins 2020 K Mallik - 2020 - preprints.org If we follow the radial structure of the SARS CoV-2 virion, a gradual fall the in the pI values is 6NB8 (+) Human S230 antigen-binding fragment light chain 6.046 to make anti-viral drugs for SARS CoV-2. From the pI consideration, application of human Interferon- ( PDB ID 1AU1
722 3kre - Molecular dynamics perspective on the protein thermal stability: A case study using SAICAR synthetase 2013 K Manjunath, K Sekar - Journal of chemical information and modeling, 2013 - ACS Publications ... PDB. The structure of SAICAR synthetase from E. coli (PDB-id: 2gqr), E. chaffeensis (PDB-id: 3kre), G. kaustophilus (PDB- id: 2ywv), M. jannaschii (PDB-id: 2z02) and P. horikoshii (PDB-id: 3u55) were considered for simulation ...
723 3kre 3r9r Structure of SAICAR synthetase from< i> Pyrococcus horikoshii</i> OT3: Insights into thermal stability 2013 K Manjunath, SP Kanaujia, S Kanagaraj? - International journal of ?, 2012 - Elsevier ... of the native and its complex from S. cerevisiae (PDB-ids: 1obg, 1obd, 2cnu, 2cnv, 2cnq), T. maritima (PDB-id: 1kut; [36]), E. coli (PDB-ids: 2gqs, 2gqr; [37]), G. kaustophilus (PDB-id: 2ywv), M. jannaschii (PDB-ids: 2z02, 2yzl), E. chaffeensis (PDB-id: 3kre), C. perfringens (PDB-id ...
724 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
725 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 ...
726 3la9 4lgo, 3s6l, 3laa Trimeric autotransporters and their ligands-structural studies 2017 K Mikula - 2017 - helda.helsinki.fi ... There is no published fullRlength structure of TAA, however, over 30 structures of TAAs fragments comprising different domains are ... Protein fragment PDB code Organism Domain Reference ... BpaA 2278R2455 3laa 3la9 B. pseudomallei FGG, HANS, Ylhead, HIN2, Neck ...
727 3oxk 3r6f, 3o0m, 3lb5, 3p0t Structural Biology for Drug Design: Applications in Two Systems 2016 KM Maize - 2016 - search.proquest.com ... Structurally, the purple HIT-like clade (4EGU, 3OXK) appears to be highly related to the known Hint proteins, whereas the remaining three HIT-like clades differ from the Hints by the addition of a long 12-15 residue C- terminal helix ... Sequence alignment alone fails to properly separate these two structural subclasses: those that draw the C-terminal helix from the same monomer (2EO4, 3LB5, 3P0T, 3O0M, 3NRD, 3OHE, 3I4S, and 3I24), and those that cross over to ...
728 3lb5 3r6f, 3p0t, 3oxk, 3o0m Structural characterization of human histidine triad nucleotide-binding protein 2, a member of the histidine triad superfamily 2013 KM Maize, CR Wagner, BC Finzel - FEBS Journal, 2013 - Wiley Online Library ... conformational change from an 'open' to a 'closed' form during catalysis [eg Protein Data Bank (PDB) code: 3BL9 ... proteins that have not been described or compared in the literature (ie PDB structures: 1XQU, 1Y23, 2EO4, 2OIK, 3ANO, 3IMI, 3I4S, 3124, 3LB5, 3L7X, 3KSV ...
729 3laa - Structure of the UspA1 protein fragment from Moraxella catarrhalis responsible for C3d binding 2019 KM Mikula, R Kolodziejczyk, A Goldman- Journal of structural biology, 2019 - Elsevier 2012) as found in SadA (2YO2, 2YNZ) (Hartmann et al., 2012) or BpaA ( 3LAA ) (Edwards et CCP4 package (Winn et al., 2011) with the structure of UspA1 165366 ( PDB : 3PR7) (Agnew Model of UspA1 299452 structure solved in this study, neck and coiled-coil domains; chain
730 3d6b - Structure of the prolyl-acyl carrier protein oxidase involved in the biosynthesis of the cyanotoxin anatoxin-a 2013 K Moncoq, L Regad, S Mann, A Mejean and O Ploux - Acta Crystallographica Section D Biological Crystallography, 2013 - scripts.iucr.org ... coordinates and structure factors have been deposited in the Protein Data Bank (PDB) as entry ...PDB code, Enzyme, Enzyme class, Source, Identity (%), Similarity (%), Rmsd (?), No. ... 3d6b, Glutaryl-CoA dehydrogenase (apoenzyme), GCD, Burkholderia pseudomallei, 27, 45, 1.88, ...
731 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, ...
732 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: ...
733 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
734 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
735 4qtp - Mycobacterium avium subsp. paratuberculosis 감염 초기 개체 검출을 위한항원 탐색 및 특성 분석 2015 박홍태, 박현의, 신민경, 조용일, 유한상 - Korean J Vet Res, 2015 - kjvr.org ... MAP의 MAP0380 유전자가 coding하고 있는 anti-sigma factor antagonist protein(PDB ID: 4qtp,TM-score ... 1. Three-dimensional structure prediction using I-TASSER server. ... 백질은 MAP1204의p60 domain으로 나타났는데(PDB ID: 3i86, TM-score: 0.547), sequence identity가 100 ...
736 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 ...
737 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 ...
738 4ed9 - Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress 2018 KS Shrimant, S Pandey, A Ansari, S Das- et Biophysica Acta (BBA, 2018 - Elsevier The structure was found similar to the homologues available including MCR ( PDB ID: 1X74), CaiB ( PDB ID: 1XA3), FRC ( PDB ID: 2VJQ), FRC ( PDB ID: 3UBM), ACOCT ( PDB ID: 4ED9 ), YfdE ( PDB ID: 4HL6 3.5. Solution structure using Small Angle X-ray Scattering (SAXS).
739 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
740 5b8i - Two SnRK2-interacting calcium sensor isoforms negatively regulate SnRK2 activity by different mechanisms 2020 K Tarnowski, M Klimecka, A Ciesielski, G Goch- Plant, 2020 - Am Soc Plant Biol Skip to main content
741 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 ...
742 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
743 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 ...
744 3laa - Multiscale multiphysics and multidomain models—Flexibility and rigidity 2013 K Xia, K Opron, GW Wei - The Journal of chemical physics, 2013 - scitation.aip.org ... The conventional dogma of sequence-structure-function2 has been seriously challenged by the ...Structures 1DF4 and 2Y7L (top) represent the high scoring structures, those with scores near 0.9. Structures 2Y7L and 3LAA (bottom) show the typical pattern for correlation scores based on parameter values for the majority of proteins. ...
745 4g6c - Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM) 2015 K Xia, K Opron, GW Wei - The Journal of chemical physics, 2015 - scitation.aip.org ... More importantly, we reveal intrinsic multiscale behavior in protein structures. ... B-factor), ie, theatomic mean-square displacement, obtained in structure determination by ... depends the crystalenvironment, solvent type, data collection condition, and structural refinement procedure ...
746 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
747 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
748 3mmt - X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism 2016 LA Dadinova, EV Shtykova, PV Konarev, EV Rodina - PloS one, 2016 - journals.plos.org ... When comparing the predicted structure of FbaB to ten of the closest structural analogs in the PDB, three fructose bisphosphate aldolase homologues were identified (PDB: 1OK6, 3MMT, 3BV4) along with four tagatose bisphosphate aldolases ...
749 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
750 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
751 5cy4 - Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence 2019 L Calvanese, F Squeglia, M Romano- Structure and, 2019 - Taylor & Francis Despite this, its structure , a dimeric molecule with each monomer adopting a compact entry 4OKE) from Mycobacterium tuberculosis against the Protein Data Bank ( PDB ) using the Coxiella burnetii (Coxbu) (3TR8, Z-score 13.8), Acinetobacter baumannii (Aciba) ( 5CY4 , Z-score
752 4k9d - The glyceraldehyde-3-phosphate dehydrogenase of the shrimp Litopenaeus vannamei: Molecular cloning, characterization and expression during hypoxia 2018 L Camacho-Jimnez, AB Peregrino-Uriarte- Marine Environmental, 2018 - Elsevier We also made a structural analysis in silico of the deduced protein from a comparative the GAPDH holoenzyme from P. versicolor solved by X-ray diffraction (2 ) ( PDB : 1SZJ, chain Finally, the LvGAPDH multimeric complex model was obtained from the former structure with the
753 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. ...
754 3ndn - Purification of Lysine Decarboxylase: A Model System for PLP Enzyme Inhibitor Development and Study 2011 LC Zohner - 2011 - digitalcommons.unl.edu ... This is inferred from the crystal structure of a bond phosphono-analogue of L-alanine (pdb 1BD0). ... contrast to 2.6 ?, for the aspartate oxygen-pyridine nitrogen in the crystal structure of ornithine decarboxylase from Lactobacillus (pdb ID 1ORD), hinting that hydrogen ...
755 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
756 4tu1 - Structure of Toxoplasma gondii fructose-1, 6-bisphosphate aldolase 2014 LE Boucher, J Bosch - Acta Crystallographica Section F: Structural …, 2014 - scripts.iucr.org ... bound to TRAP (PDB entry 2pc4 , chain D) and TgAldolase (PDB entry 4tu1 , chains A ... highlightsthe residues important for adhesin binding in the TRAP-bound PfAldolase structure (PDB entry2pc4 ... to -helix 10 in chain A does not align with the PfAldolase structure; however, the ...
757 4tu1 3sth The apicomplexan glideosome and adhesins–Structures and function 2015 LE Boucher, J Bosch - Journal of structural biology, 2015 - Elsevier The apicomplexan family of pathogens, which includes Plasmodium spp. and Toxoplasma gondii,are primarily obligate intracellular parasites and invade multiple c.
758 3o2e - Phosphorylation status of BolA affects its role in transcription and biofilm development 2021 L Galego, S Barahona, CV Romo- The FEBS, 2021 - Wiley Online Library NMR structure of mouse BolA1 ( PDB ID 1V60) and E. coli BolA ( PDB ID 2DHM) reveal a structure with similarity to nucleic acid binding proteins including a helix-turn [6]. MreB is a structural homologue of actin that is essential for cell elongation, maintenance of
759 3ek1 3i44 Residues that influence coenzyme preference in the aldehyde dehydrogenases 2015 L González-Segura, H Riveros-Rosas… - Chemico-biological …, 2015 - Elsevier ... enzymes. 2. Methods. 2.1. Structural comparisons. Structural comparisons of the ALDHcrystal structures available in the PDB were made using PyMOL (http://www.pymol.org) and Coot [10]. 2.2. Sequence analyses. ALDH amino ...
760 4ohc - Orotato fosforribosiltransferasa. Pasado, presente y futuro en el estudio estructural de las protenas. 2020 L Gonzlez-Segura, EI Carrizosa-Carbajal - bq.facmed.unam.mx Past, present and future in the structural study of proteins Key words: Phosphoribosyltransferase; three- dimensional structure ; conformational change; inhibition; pyrimidines synthesis str (PDBs 3M3H y 4RV4), de Burkholderia cenocepacia ( PDB 4OHC ), de Corynebacterium
761 3ek1 3i44 Potential monovalent cation-binding sites in aldehyde dehydrogenases 2013 L Gonz?lez-Segura, H Riveros-Rosas? - Chemico-biological Interactions, 2013 - Elsevier ... Cation-binding sites. Family/organism, PDB code, Resolution (?), Monovalent cation in protein solution/crystallization solution, Intra, Inter, Central-cavity a. ... Brucella melitensis, 3EK1, 2.10, nr/(NH 4 ) 2 SO 4 1 M, Proposed (Water ? Na + ), Proposed (Water ? Na + ) i, No (Lys at 479 ...
762 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.
763 4j5i - Structural Studies in Natural Product Biosynthesis and Structure Determination 2016 L Han - 2016 - scholarship.rice.edu Page 1. Page 2. ABSTRACT Structural Studies In Natural Product Biosynthesis And Structure Determination by Lu Han Natural living organisms produce many natural compounds with diverse structures . They are one of the most productive sources of drug/bio-probe ... Taurine dioxygenase TauD from Mycobacterium smegmatis, Z= 17.5, r.m.s.d. 3.0Å over aligned Cα residues, id 15% (PDB 4J5I) (Baugh et al., 2015).
764 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)).. ...
765 3laa - Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen 2015 LJ Gourlay, C Peano, C Deantonio - Section D: Biological , 2015 - scripts.iucr.org ... 1 [link] , Supplementary Tables S1 and S2). The 1.8 resolution crystal structure of BPSL2063Xtal was solved by molecular replacement using the structure of BpaA (PDB entry 3laa ; Edwardset al., 2010 [Edwards, TE, Phan, I., Abendroth, J., Dieterich, SH, Masoudi, A ...
766 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. ...
767 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
768 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
769 3dah 3kjr, 3i3r Multiparameter screening on slipchip used for nanoliter protein crystallization combining free interface diffusion and microbatch methods 2009 L Li, W Du, RF Ismagilov - Journal of the American Chemical Society, 2009 - ACS Publications ... The crystal structure was determined at 2.3 ? resolution (PDBid: 3DAH). ... 37 mM sodium citrate, pH 5.5) yielding crystals in space group P4 3 2 1 2. We obtained a data set at 1.83 ? with crystals produced by scaling up, and the structural determination and PDB deposition are in ...
770 3d6b 3ii9 User-loaded SlipChip for equipment-free multiplexed nanoliter-scale experiments 2009 L Li, W Du, R Ismagilov - Journal of the American Chemical Society, 2009 - ACS Publications ... These crystals yielded a structure of 2.2 ? resolution and space group P2 1 2 1 2 1 (PDBid3D6B). Without ... manuscript. We thank Bart Staker for checking the structure of glutaryl-CoA dehydrogenase for PDB deposition. Supporting Information ...
771 4dhe - Molecular dissection of the interface between the Type VI secretion TssM cytoplasmic domain and the TssG baseplate component 2016 L Logger, MS Aschtgen, M Gurin, E Cascales - Journal of Molecular , 2016 - Elsevier ... a C-terminal extension (Ct, green). TssM Cyto/NTP was modelled using HHpredbased on the X-ray structure of the Burkholderia thailandensis EngB GTP-bindingprotein (PDB ID: 4DHE). TssM Cyto/Ct was modelled using ...
772 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 ...
773 4i1v - Tethering of Epidermal Growth Factor (EGF) to Beta Tricalcium Phosphate (βTCP) via Fusion to a High Affinity, Multimeric βTCP-Binding Peptide: Effects on … 2015 LM Alvarez, JJ Rivera, L Stockdale, S Saini, RT Lee… - PloS one, 2015 - dx.plos.org ... The TT motif has been implicated in the interactions of dephospho-CoA kinases with the diphosphate group of adenosine di-phosphate (ADP) through hydrogen bonding mechanisms (PDB ID#s: 1JJV, 4I1V; [83]), suggesting a potential role for the TT motif in our binding peptide for interaction with calcium phosphate ...
774 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 ...
775 3tjr - On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment 2020 LM Longo, J Jablonska, P Vyas, R Kolodny, N Ben-Tal- bioRxiv, 2020 - biorxiv.org between Rossmanns and P-loops, ideally with respect to not only structure but also sequence 2003.1.1.417; PDB : 1k2w) and short chain dehydrogenase (F-Group 2003.1.1.332; PDB : 3tjr ) showing the highest overlap (Figure 4)
776 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).
777 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
778 3sds - New Insight into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine 2012 LM Polo, F Gil-Ortiz, A Cant?n, V Rubio - PloS one, 2012 - dx.plos.org ... the closest structures to that of the PTC subunit those of the subunits of pfOTC, Thermotoga maritima OTC (tmOTC) and hOTC, (Protein Databank files 1PVV ... PDB files are the following for OTCs: human, 1OTH; Ovis aries, 1FB5; Coccidioides immitis, 3SDS; P. furiosus1PVV ...
779 3meq - Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD 2013 LM Thomas, AR Harper, WA Miner? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... 2007). J. Appl. Cryst. 40, 658-674.] ). The structure of Brucella melitensis alcohol dehydrogenase (PDB entry 3meq ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) was used as the initial model. The ...
780 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. ...
781 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
782 3eg4 - The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism 2009 L Schuldt, S Weyand, G Kefala, MS Weiss - Journal of molecular biology, 2009 - Elsevier ... coli (PDB entry 3BXY), 7 Campylobacter jejuni (PDB entry 2RIJ, Joint Center for Structural Genomics, unpublished results), Enterococcus faecalis (PDB entry 3CJ8, K. Tan et al., unpublished results) and Brucella melitensis biovar abortus (PDB entry 3EG4, Seattle Structure ...
783 5dd7 - Structural and inhibition studies of thiamine monosphosphate kinase from Mycobacterium tuberculosis 2020 LS Dlamini - 2020 - repository.up.ac.za OT Oxythiamine PDB Protein data bank 38 Figure 3.5: Crystal structure of MtbThiL homodimer ..... 40 bind to both free enzyme and the ES complex. Detailed structural information particularly high resolution crystal structures of substrate
784 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..
785 4mei 4jf8, 4lso, 4kz1, 4o3v, 4nhf Structural and Molecular Biology of Type IV Secretion Systems 2017 L Terradot, C Berg, G Waksman- Type IV Secretion in Gram-Negative, 2017 - Springer 1.2 Composition of T4SSs. X-ray crystallography, nuclear magnetic resonance (NMR), and more recently electron microscopy have been successfully used to provide insights into the structure of T4SSs Plasmid or bacteria. PDB or EMDB ID 4KZ1,4JF8,4LSO, 4MEI ,4NHF m
786 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
787 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
788 4ffc - Polyamines in Fungi: Their Distribution, Metabolism, and Role in Cell Differentiation and Morphogenesis 2015 L Valds-Santiago, J Ruiz-Herrera - 2015 - books.google.com ... of Polyamines.....5 2.1 Introduction.....5 2.2 Chemical Structure and Physicochemical ... of theInteractions of Polyamines with Cell Macromolecules and Structures..... ...
789 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
790 4xgi - Rational engineering of Acinetobacter tandoii glutamate dehydrogenase for asymmetric synthesis of l-homoalanine through biocatalytic cascades 2021 L Wang, S Diao, Y Sun, S Jiang, Y Liu- Catalysis Science &, 2021 - pubs.rsc.org on the crystal structure of GluDH from Burkholderia thailandensis ( PDB ID: 4XGI , resolution: 2.0 ) in symbiosum ( PDB ID: 1AUP and 1BGV) and GluDH from Corynebacterium glutamicum ( PDB ID: 5IJZ amino acid may cause loss of the inherent stability of the hydration structure
791 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. ...
792 5cy4 - Structural insights into nanoRNA degradation by human Rexo2 2019 LY Chu, S Agrawal, YP Chen, WZS Yang, HS Yuan- RNA, 2019 - rnajournal.cshlp.org 6A4E), or deposited in the protein data bank, including those from E. coli ( PDB codes: 1YTA, 2IGI), Acinetobacter baumannii ( PDB code: 5CY4 ), and Haemophilus influenzae ( PDB code 1J9A) Structural coordinates and diffraction structure factors of Rexo2-RNA, Rexo2-DNA1
793 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
794 3tv2 3gtd, 3qbp, 3rd8 Structural, biochemical and biophysical characterization of recombinant human fumarate hydratase 2019 MA Ajalla Aleixo, VL Rangel, JK Rustiguel- The FEBS, 2019 - Wiley Online Library code: 3GTD; [37]), Burkholderia pseudomallei FH (BpFH, PDB code: 3TV2 ; results not (MsFH, PDB code: 3RD8; [38]). The superposition of C atoms between HsFH and the From the structure -based drug design perspective, it is imperative to identify
795 4u7x - Mrub_3029, Mrub_2052, are predicted orthologs of b_0688, b_0394, while Mrub_0759 and Mrub_2365 are not predicted orthologs of b_1309, in Escherichia 2017 MA Benstine, D Scott, R Lori - 2017 - digitalcommons.augustana.edu Next, the Protein Data Bank ( PDB ) is accessed which gives 3-D models of protein structures our gene is found in, it helps portray how the protein is folded which helps predict function (Bernman et al, 2003) Protein Database ( 4U7X ) Crystal structure of Fructokinase from
796 4u7x - Mrub_3029, Mrub_2052, are predicted orthologs of b_0688, b_0394, while Mrub_0759 and Mrub_2365 are not predicted orthologs of b_1309, in Escherichia coli, 2017 MA Benstine, D Scott, R Lori - 2017 - digitalcommons.augustana.edu ... Next, the Protein Data Bank (PDB) is accessed which gives 3-D models of protein structures ourgene is found in, it helps portray how the protein is folded which helps predict function (Bernmanet al, 2003). ... Protein Database (4U7X) Crystal structure of Fructokinase from ...
797 3rd5 - Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells 2015 M Abu-Remaileh, E Joy-Dodson - Journal of Biological , 2015 - ASBMB ... B, a structural model of the SDR region (generated by the RosettaCM protocol as implemented by the Robetta server (78), starting from PDB ID 3rd5 (58) as a template structure) shows an extended central β sheet formed by Rossmann folds. ...
798 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 ...
799 6tys - Structural insight into paramyxovirus and pneumovirus entry inhibition 2020 M Aggarwal, RK Plemper- Viruses, 2020 - mdpi.com 19,20,21] have furthermore created a novel opportunity for structure -informed mechanistic Structural information is very limited compared to that available for the paramyxovirus attachment Consequently, crystal structures of prefusion PIV5 and NiV F ectodomains could only be
800 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
801 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
802 5bq2 - Molecular modelling and dynamic simulation of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) from Mycobacterium tuberculosis using in silico 2018 MA Isa, RS Majumdar, S Haider- Informatics in Medicine, 2018 - Elsevier structure of UDP-N-acetylglucosamine -1-carboxyvinyltransferase (MurA) is not available in PDB . Therefore, the 3D structure was determined through the sequence, obtained from NCBI (Accession result of a BLASTp search against PBD, six proteins (3SG1, 5BQ2 , 3ISS, 1A2N
803 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
804 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 ...
805 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
806 4ix8 - Tyrosine aminotransferase from< i> Leishmania infantum</i>: A new drug target candidate 2014 MA Moreno, A Alonso, PJ Alcolea, A Abramov - International Journal for , 2014 - Elsevier ... code: 3DYD) and the mouse TAT (PDB code: 3PDX) ( Mehere et al., 2010). Recently, the structure of LiTAT has been solved to 2.3 (PDB code: 4IX8) ( Moreno et al., 2014). On the basis of this background, the aim of the work is ...
807 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). ...
808 2klx 3fq3, 3hhj Potential druggable proteins and chimeric vaccine construct prioritization against Brucella melitensis from species core genome data 2019 M Aslam, M Shehroz, M Shah, MA Khan, SG Afridi- Genomics, 2019 - Elsevier The radius of gyration was also predicted to assess the compactness of structure and the Gene symbols, PDB homolog ID's, Protein Names, Model C-score, Template Vs model RMSD BME_RS00875, 2KLX , glutaredoxin 3, 0.89, 2.0 1.6 , 98.718, 2.88, 0.99 (26), 9419.75, 3.27
809 6q04 6VXX N-terminal domain (NTD) of SARS-CoV-2 spike-protein structurally resembles MERS-CoV NTD sialoside-binding pocket 2020 M Awasthi, S Gulati, DP Sarkar, S Tiwari, S Kateriya - 2020 - researchsquare.com W program [14]. Structure preparation The cryo-EM structures of SARS-CoV-2 ( PDB ID: 6VXX) [8] and MERS-CoV ( PDB ID: 6Q04 ) [10] spike spike glycoprotein (YP_009724390. 1) was strongly biased on the crystal structure of SARS-CoV-2, while
810 6q04 6VXX The sialoside-binding pocket of SARS-CoV-2 spike glycoprotein structurally resembles MERS-CoV 2020 M Awasthi, S Gulati, DP Sarkar, S Tiwari, S Kateriya- Viruses, 2020 - mdpi.com Multiple sequence alignment of the NTD domains was performed with the Clustal W program [15]. 2.2. Structure Prediction. The cryo-EM structures of SARS-CoV-2 ( PDB ID: 6VXX) [8] and MERS-CoV ( PDB ID: 6Q04 ) [11] spike glycoproteins were used as the starting point for
811 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
812 5j3b - Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System 2020 MB Bertelsen, M Senissar, MH Nielsen, F Bisiak- Structure, 2020 - Elsevier Here, we provide structural insights into the architecture of the intact VapXD TA complex and toxin residues missing in each chain likely due to flexibility (Figure S1A). The structure consists of PDB Entry, VapXD (Selenomethionine) 6ZN8, VapD (Wild Type) 6ZI0, VapD (D7N) 6ZI1... (B) Structure of the Acinetobacter baumannii EF-P OB fold with conserved secondary structure in gold (PDB: 5J3B, left) and corresponding topology (right).
813 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
814 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
815 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 ...
816 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
817 6mb1 - Profiling of myristoylation in Toxoplasma gondii reveals an N-myristoylated protein important for host cell penetration 2020 M Broncel, C Dominicus, L Vigetti, SD Nofal, EJ Bartlett- Elife, 2020 - elifesciences.org structure with bound IMP-1002 ( PDB : 6MB1 , [Schlott et al., 2019]) revealed high sequence identity (57%) and showed that all residues directly involved in compound binding are conserved within the TgNMT active site and therefore predicted to adopt an identical structural
818 2kwl 2lol, 2lky, 2l3v Protein packing defects heat up interfacial water 2013 MB Sierra, SR Accordino, JA Rodriguez-Fris? - The European Physical Journal E, 2013 - Springer ... 2BZT, 2eyz, 2FDQ, 2GEQ, 2jqx, 2JQY, 2JU6, 2K0P, 2K4Q, 2KJG, 2KV4, 2KWD, 2KWL, 2L3V, 2L4V ... ex- plicitly the situation for one of the proteins studied: the p53 protein (PDB 2GEQ ... this molecule represents one of the largest dehydron clusters in the Protein Data Bank [9]. From ...
819 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
820 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
821 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. ...
822 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 ...
823 5k85 - Selective inhibition of Zophobas morio (Coleoptera: Tenebrionidae) luciferaselike enzyme luminescence by diclofenac and potential suitability for lightoff 2020 MC Carvalho, A Tomazini, RA Prado- Luminescence, 2020 - Wiley Online Library tertiaricarbonis PDB file ID: 6HE0, Cryptococcus neoformans PDB file ID: 5K85 , Salmonella typhimurium PDB file ID: 5JRH) indicated that, among the five binding sites, that of CoA was structure and function prediction. Nat Protoc 2010; 5: 25-738. 49
824 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
825 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
826 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...
827 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
828 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
829 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. ...
830 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. ...
831 4fkx - Protein Secondary Structure Detection Using Dihedral Angle Parameters Evaluation 2014 M Diez, V Petuya, I Mart?nez, A Hern?ndez - The 11th IFToMM International Symposium on Science of Mechanisms and Machines Mechanisms and Machine Science , 2014 - Springer ... To check the results obtained with the procedure, they have been compared with each proteins' structural data, available on the Protein Data Bank (PDB) and experimentally obtained. ... 1zac. 96.6. 1k9p. 96.62. 3cln. 97.2. 1k20. 93.48. 2peq. 100. 4fkx. 82.35. 3sza. 86.6. ...
832 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 ...
833 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
834 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 ...
835 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). ...
836 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;
837 3u03 - Pyoverdine, the Major Siderophore in Pseudomonas aeruginosa, Evades NGAL Recognition 2012 ME Peek, A Bhatnagar, NA McCarty? - Interdisciplinary Perspectives on Infectious Diseases, 2012 - hindawi.com ... Recently, Strong and coworkers crystallized NGAL bound to pyochelin (PDB 3U03, deposited at the RCSB protein data bank) and the crystal structure clearly shows that pyochelin docks inside the calyx of NGAL but without binding avidly. ...
838 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
839 4dz6 3gp5, 3gw8 Structural and functional studies on the reactivity of CORMs with plasma proteins 2016 MFA Santos - 2016 - run.unl.pt ... 1.37 Structural representation of the vanadate(V)-RNase A adduct (PDB: 1RUV)52 ... Figure 2.7 Overall structure of HEWL bound to Ru fragments derived from ALF850 ... Figure2.8 Structural representation of RuHis15 adduct85 ...
840 4jpd - SAXS and stability studies of iron-induced oligomers of bacterial frataxin CyaY 2017 M Fekry, W Alshokry, P Grela, M Tchrzewski- PloS one, 2017 - journals.plos.org ... The crystal structure of the CyaY monomer ( PDB entry 1EW4) was used for building a model, which was assumed to be a ... The ratio between the emission intensities at 350 nm and 330 nm (F350/F330) was used to track the structural changes with increasing temperature. ...
841 4qgr 3njd Prediction of homoprotein and heteroprotein complexes by protein docking and templatebased modeling: A CASPCAPRI experiment 2016 MF Lensink, S Velankar - Proteins: Structure, , 2016 - Wiley Online Library ... Next article in Early View: Critical assessment of methods of protein structure prediction: Progressand new directions in round XI. ... E-mail: marc.lensink@univ-lille1.fr or Shoshana J. Wodak; VIBStructural Biology Research Center, VUB, 1050 Brussels, Belgium. ...
842 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
843 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). ...
844 5ihp - Structural studies of the DNA partitioning protein IncC from the plasmid RK2 2018 MFU Rehman - 2018 - etheses.bham.ac.uk Page 1. Structural Studies of the DNA Partitioning Protein IncC from the Plasmid RK2 By 251 6.15.2 Crosslink- structure mapping using IncC2 models 23 1.16 Structures of DNA/centromere binding proteins (CBP) 25 1.17 C- and N- terminals of KorB protein
845 3p4t - Mycobacterium tuberculosis cholesterol catabolism utilizes a structurally and evolutionarily discrete class of acyl-Coenzyme A dehydrogenase 2015 MF Wipperman - 2015 - search.proquest.com This image (grey) shows the crystal structure of tetrameric FadE13 from M smegmatis (pdb: 3P4T) using the DAMAVER modeling algorithm.
846 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
847 3k2h - Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance 2018 MG Corral, J Haywood, LH Stehl, KA Stubbs- The Plant, 2018 - Wiley Online Library The homology models of A. thaliana DHFR‐TS1 and DHFR‐TS2 were created ab initio based on the structure of the bifunctional DHFR‐TS enzyme from B. bovis (PDB 3K2H; Begley et al., 2011), using the I‐TASSER server (Zhang, 2008).
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