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 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 ...
2 2ke0 - In silico prediction of binding sites on proteins 2010 S Leis, S Schneider, M Zacharias - Current medicinal chemistry, 2010 - ingentaconnect.com ... 15 Leis et al. Table 3. Protein Test Structures pdb entry molecule state ligand Rmsd (?)b 2ANO E.coli dihydrofolate reductase bound Inh. MS-SH08-17 0 ... 1FKS_2VCD 1FKS based on 2VCD structure homology --- 2.3 1FKS_2KE0 1FKS based on 2KE0 structure homology --- 2.6 ...
3 2khp - Identifying selective ligands for glutaredoxin proteins with fragment based drug design approach and optimization of the bacterial selective hits 2016 RB Khattri - 2016 - etd.ohiolink.edu ...These were compared to structures deposited in the Protein Data Bank (RCSB PDB). The PBD name for the BrmGRX is 2KHP (Leeper et. al, 2011) and hGRX1 is 1JHB (Sun et. al, 1998).. ...
4 2khp - An NMR-guided screening method for selective fragment docking and synthesis of a warhead inhibitor 2016 RB Khattri, DL Morris, CM Davis, SM Bilinovich - Molecules, 2016 - mdpi.com ... The active site architecture of BrmGRX matches with the proposed GRX consensus active sitestructure which suggests the N ... Structures of target proteins were obtained from the Protein DataBank (PDB) [63]. The PBD code for BrmGRX is 2KHP and hGRX1 is 1JHB [19,64]. ...
5 2khp - Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead 2020 RB Khattri, DL Morris, SM Bilinovich, E Manandhar- Molecules, 2020 - mdpi.com between the two domains, the presence of multiple paralogs in one or both species, and a lack of conserved genomic architecture between the Structural comparison of hGRX1 to E. coli GRX and BrmGRX indicated similarities in the overall fold and structure ... NMR backbone resonance assignments for BrmGRX (2KHP) and hGRX1 (1JHB) were obtained from the BMRB
6 2khp - Nuclear Magnetic Resonance Spectroscopy in the Study of Protein Complexes 2014 SM Bilinovich - 2014 - rave.ohiolink.edu ... Molecular simulations and docking studies were performed using the pdb coordinates of the NMR determined structure of Brucella melitensis GRX (pdb 2KHP) (Leeper et. al 2011). Autodocking was performed using a copper(I) ion ...
7 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. ...
8 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 ...
9 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.
10 2khr 2kvc Investigating conformational transitions of proteins by coarse-grained elastic network models 2012 M Tekpinar - 2012 - search.proquest.com The model is the green tube representation and the target ( PDB ID: 1LST) is the dark blue tube. Residues 91 B- factors show that each atom in the structure is dynamic in side chains of their amino acids. However, some conformations can have large structural
11 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
12 2klx - Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta 2019 ML Aprahamian, S Lindert- Journal of Chemical Theory and, 2019 - ACS Publications like the following: Which amino acid types provide the most useful structural information structures that served as a nonredundant representation of single chain monomers in the PDB the protein set, distributions of the total number of residues, secondary structure content... The six proteins selected from the ab initio set were PDB ID 1tpm, 2klx, 2nc2, 2y4q, 3iql, and...
13 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
14 2klx - Studies in Computational Biochemistry: Applications to Computer Aided Drug Discovery and Protein Tertiary Structure Prediction 2019 ML Aprahamian - 2019 - rave.ohiolink.edu structures were identified using a receiver operator characteristic (ROC) analysis and a set of known binding compounds. Using these structures as the receptors for structure -based drug discovery, a virtual screen was performed on the National Cancer Institute's ... The six proteins selected from the ab initio set were PDB ID 1tpm, 2klx, 2nc2, 2y4q, 3iql, and 4omo.
15 2kn9 - Redox Proteins of Mycobacterium tuberculosis 2014 S Phulera, M Akif, AA Sardesai? - Journal of the Indian Institute of Science, 2014 - journal.iisc.ernet.in ... The individual structures shown are (A) NrdH, pdb id: 4HS1, (B) FurB, pdb id: 2O03, (C) DipZ,pdb id: 2HYX, (D) FcoT, pdb id: 2PFC, (E) AhpD, pdb id: 1KNC, (F) Mycoredoxin, pdb id: 2LQQ, (G) Rubedoxin C with Zinc atom shown as sphere, pdb id: 2KN9, (H) TrxC, pdb id: 1LU4 ...
16 2kn9 - A new twist of rubredoxin function in M. tuberculosis 2020 T Sushko, A Kavaleuski, I Grabovec, A Kavaleuskaya- bioRxiv, 2020 - biorxiv.org 21]. Previously, a zinc-substituted RubB structure was solved by NMR ( PDB ID: 2KN9 ). Pairwise . In the NMR model, residues at C and N termini show backbone variability, while the rest of the structure remain almost unperturbed
17 2kn9 - Structure Based Computational Exploration of Beilschmiedia Compounds with Selected Targets against Multidrug-Resistant Mycobacterium tuberculosis 2019 M Yasir, P Singh, S Chohan, R Shrivastava- INDIAN JOURNAL OF, 2019 - ijper.org Protein Name PDB - ID Binding Energy (kcal/mol) Antigen 85C 1dqz -3.34 Cytochrome P450 Crystal structure of 3-bromopyruvate modified isocitrate lyase (icl) 1f8m -2.09 EmbR 2ff4 -4.38 Hydroxymycolate synthase MmaA4 2fk7 - Zinc-substituted rubredoxin B 2kn9 -3.46 Cell
18 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).
19 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.
20 2kn9 - Metodos Computacionais para o Calculo de Estruturas de Proteinas: Aproximando o Problema Molecular de Geometria de Distancias de Dados de Ressonancia Magnetica Nuclear 2010 PC Nucci - ic.uff.br ... PMGD Problema Molecular de Geometria de Dist?ncias PMGDD Problema Molecular de Geometria de Dist?ncias Discreto BP Branch-And-Prune RMN Resson?ncia Magn?tica NuclearPDB Protein Data Bank pH Potencial Hidrogeni?nico 12 Page 14. Cap??tulo 1 Introdu??ao ...
21 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 ...
22 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
23 2kok - A deep learning approach to the structural analysis of proteins 2019 M Giulini, R Potestio- Interface focus, 2019 - royalsocietypublishing.org Second, we show that the application of a simple, standard and computationally not expensive DL architecture to the selected features gives satisfactory results, suggesting that The raw data employed in the present work, including PDB files, protein structure datasets, CNN ... Eigenvalues associated with 2KOK, 2YQD, and 1MEK were predicted with reasonable accuracy, the overall average MAPE being 30.7, 35.5 and 48.3, respectively.
24 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). ...
25 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 ...
26 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,
27 2kok - A new arsenate reductase involved in arsenic detoxification in Anabaena sp. PCC7120 2013 S Pandey, AK Shrivastava, VK Singh, R Rai… - Functional & integrative …, 2013 - Springer ... b Structure-based multiple sequence alignment of All0195 homologs. ... 261278552
28 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. ...
29 2kwl 2lol, 2lky Aspectos estructurales y dinmicos en la relajacin de sistemas complejos, con nfasis en agua lquida, sobreenfriada y nanoconfinada 2015 SR Accordino - 2015 - repositoriodigital.uns.edu.ar prctico: previene la agregacin de dos placas de grafeno. Page 9. 9 Abstract In this Thesis we studied, by means of molecular dynamic simulations, the structural and We also determined the geometrical quality of the local structure of these kinds of molecules. In
30 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 ...
31 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 ...
32 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 ...
33 2kwl 2l4b Cloning, expression and characterisation of the starter module from indanomycin biosynthesis 2014 SR Derrington - 2014 - etheses.whiterose.ac.uk Both structure calculations produced comparable structures for IdmK. The structure 137 4.5 Structure determination using NMR spectroscopy ..... 139 4.5.1 Initial analysis of the suitability of IdmK for structural studies by NMR ... Further validation was carried by comparison with known canonical acyl carrier protein folds (PDB codes: 1HY8, 1T8K, 1VKU, 2AVA, 2CGQ, 2GDW, 2KOO, 2KWL and 2L0Q) (X
34 2kz0 2mcq Structural and spectroscopic insights into BolA-glutaredoxin complexes 2014 T Roret, P Tsan, J Couturier, B Zhang - Journal of Biological Chemistry, 2014 - ASBMB ... and the AtGrxS14-BolA2 apo-heterodimer model (2MMA) are available at the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank. ... Accordingly, in Ehrlichia chaffeensis and Rickettsia prowazekii BolA structures (PDB entry 2KZ0 and 2MCQ ...
35 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
36 2lbb 2l4b Physical Folding Codes for Proteins 2019 X Ma, C Hou, L Shi, L Li, J Li, L Ye, L Yang- arXiv preprint arXiv, 2019 - arxiv.org 15 Soares, CM, Teixeira, VH & Baptista, AM Protein Structure and Dynamics in Nonaqueous Solvents: Insights from Nature Structural Biology 10, 980, doi:10.1038/nsb1203-980 (2003 JL The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
37 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...
38 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
39 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 ...
40 2lwk - Viral RNA targets and their small molecule ligands 2017 T Hermann- RNA Therapeutics, 2017 - Springer disrupt or stabilize the RNA hairpin and thereby affect the equilibrium between translation of structural and enzymatically The three-dimensional structure of the FFS RNA in complex with a synthetic compound has been The added tetraloop is indicated in grey ( PDB : 2LWK ) [34]
41 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
42 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)
43 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
44 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
45 2lwk - Recent Advances in Developing Small Molecules Targeting Nucleic Acid 2016 M Wang, Y Yu, C Liang, A Lu, G Zhang - International journal of molecular , 2016 - mdpi.com ... Figure 12A) consists of a planar ring, an amino sugar structure and a fused cyclohexane ringsystem. A lot of structural studies have been investigated to understand the interaction betweenDNA duplex and molecule [28,46,47,48,49,50,51]. Most of the structures indicate that ...
46 2lwk - Using Machine Learning to Better Predict the Structure of RNA and RNA Containing Complexes 2020 S Chhabra - 2020 - deepblue.lib.umich.edu 53 3.5 Top 10 RNA Structures for 2LWK predicted from sequence using CS-Fold and Rosetta structures . The statistics from Protein Data Bank ( PDB ) (http://www.rcsb.org) current understanding of the RNA structure -function relationships is limited due to
47 2lwk - Small molecules targeting viral RNA 2016 T Hermann - Wiley Interdisciplinary Reviews: RNA, 2016 - Wiley Online Library ... The added tetraloop is indicated in gray. (c) Detail view of the ligand binding site in theNMR model, showing hydrogen atoms of the ligand 11. Structure images were preparedfrom PDB coordinate file 2LWK.[48]. Download figure to PowerPoint. ...
48 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. ...
49 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 )
50 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
51 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). ...
52 2lwk - Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions 2015 YZ Shi, L Jin, FH Wang, XL Zhu, ZJ Tan - Biophysical journal, 2015 - Elsevier TABLE 1 The 32 RNA Molecules for 3D Structure Prediction in This Work 26 2LWK ...
53 2lxf - Machine Learning-assisted Prediction of Structure and Function of Cystine-stabilized Peptides and Optimization of Expression in an E. coli System 2018 SMA Islam - 2018 - search.proquest.com Each type is annotated with its name, PDB id, function and jmol estimated average 3D structural distance between disulfide bonds PBS Phosphate buffered saline PDB Protein data bank QSAR Quantitative structure activity relationship QSO Quasi-sequence-order
54 2m4y - Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches 2016 T Sikosek, H Krobath, HS Chan - PLoS Comput Biol, 2016 - journals.plos.org ... (f) Rubredoxin type protein from Mycobacterium ulcerans (PDB:2M4Y). (g) Pancreatic secretory trypsin inhibitor (Kazal type) variant 3 (PDB:1HPT) ...
55 2mcq 2kz0 Structural and spectroscopic insights into 2014 N Rouhier, C Didierjean, BZ Couturier, MK Johnson - 2014 - ASBMB ... it seems also that the side-chain of an arginine residue (R127 in AtBolA1) present in α3-helixis involved in tertiary structure maintenance (Fig. ... Accordingly, in Ehrlichia chaffeensis andRickettsia prowazekii BolA structures (pdb entry 2KZ0 and 2MCQ respectively), two ...
56 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
57 2mj3 - Structural and functional characterisation of ferredoxins in Bacillus cereus 2015 S Monka - 2015 - duo.uio.no ...as well as testing out models generated from several homologous PDB-structures. This server generated models from 10 PDB files (1I7H, 3AH7, 3ZYY, 1KRH, 3N9Z, 2MJ3, 3HUI, 2Y5C, 1JQ4, 2WLB15) and generated two models from each by using two different programs SCULPTURE and MOLREP. ...
58 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
59 2mu0 2kok Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters 2020 MR Rosen, JB Leuthaeuser, CA Parish, JS Fetrow- Biochemistry, 2020 - ACS Publications Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs).... We performed MD simulations to better understand the conformational behavior of each of the nine classes of proteins identified by autoMISST. Starting structures for these simulations were obtained from the following data available in the RCSB PDB:34 group 3AAA, 2KOK (chain A); group 4AA, 2MU0 (chain A); gro
60 2n3s - Solution structure of protein synthesis initiation factor 1 from Pseudomonas aeruginosa 2016 Y Hu, A Bernal, JM Bullard, Y Zhang - Protein Science, 2016 - Wiley Online Library ... from: E. coli (PDB 1AH9), M. tuberculosis (PDB 3I4O), S. pneumoniae (PDB 4QL5), B.thailandensis (PDB 2N3S), T. thermophilus (PDB 1HR0). Secondary structural elements,highlighted in gray, were derived from the PDB structures. The secondary structure elements ...
61 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
62 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
63 2n6t 2n6s, 2n6x, 2n6w F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly 2017 S Jain, T Schlick- Journal of molecular biology, 2017 - Elsevier Table 1. List of 50 RNA PDB files whose 3D structures were generated in this paper. PDB , Residues, Molecule, Structure . 2M4W, 17, HEV genome bulge, Hairpin, internal loop 2N6T , 42, CssA mRNA thermometer top, Hairpin, internal loops
64 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. ...
65 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 ...
66 3cez - Structure-functional Characterization of Mammalian Redox Proteins: Methionine sulfoxide reductase B1 (MsrB1), Glutaredoxin domain (Grx) of TGR, and Thioredoxin (Trx) 2013 O Dobrovolska - 2013 - ntnu.diva-portal.org ... situated in the second ?-sheet. The four cysteines Cys23, Cys26, Cys71, and Cys74, situated outside the protein active site, coordinate zinc ion, stabilizing the structure of MsrB1. Figure II.1.2. Structure of MsrB1 (pdb code 2kv1) [55]. II.1.1 MsrB1-Thioredoxin interaction ...
67 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 ...
68 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
69 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).
70 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 ...
71 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 ...
72 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. ...
73 3cez - Structural and kinetic analysis of an MsrA-MsrB fusion protein from Streptococcus pneumoniae 2009 YK Kim, YJ Shin, WH Lee, HY Kim? - Molecular Microbiology, 2009 - Wiley Online Library ... The Protein Data Bank accession codes for other Msr proteins discussed in this article are as follows: BtMsrA (1FVA), EcMsrA (1FF3), MtMsrA (1NWA), NmMsrA (3BQE, 3BQF, 3BQH), PtMsrA (2J89), BsMsrB (1XM0), BpMsrB (3CEZ, 3CXK) and NgMsrB (1L1D). Kinetic assays. ...
74 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
75 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. ...
76 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 ...
77 3cxk - Methionine sulfoxide reduction in ciliates: Characterization of the ready-to-use methionine sulfoxide-< i> R</i>-reductase genes in< i> Euplotes</i> 2013 N Dobri, EEN Oumarou, C Alimenti, C Ortenzi? - Gene, 2012 - Elsevier ... The crystallographic structure of the Burkholderia pseudomallei MsrB (PDB ID: 3cxk) was automatically selected by the server as a template since it shows an amino acid sequence identity of 53% and 56% with the MsrB protein of E. raikovi and E. nobilii, respectively. ...
78 3cxk - Functional characterization of methionine sulfoxide reductases from Leptospira interrogans 2020 N Sasoni, MD Hartman, SA Guerrero- et Biophysica Acta (BBA, 2020 - Elsevier The Met oxidation could change the structure and function of many proteins, not only of those redox-related but also of others involved in different metabolic pathways. Until now, there is no information about the presence or function of Msrs enzymes in Leptospira interrogans
79 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 ...
80 3d53 3ome Identification of two-histidines one-carboxylate binding motifs in proteins amenable to facial coordination to metals 2012 M Schmid, G Collet, P Cuniasse, F Gilardoni? - Metallomics, 2012 - pubs.rsc.org ... 60% sequence similarity are indicated by a * PDB code, Annotated protein function, Carboxylate, Histidine 1, Histidine 2. ... Aminocarboxypropyl-transferase, Glu86*, His193*, His195*. 3D53, Pyrophosphatase, Asp114*, His76*, His77*. ...
81 3d53 3oc6 Enzyme repurposing of a hydrolase as an emergent peroxidase upon metal binding 2015 N Fujieda, J Schätti, E Stuttfeld, K Ohkubo, T Maier… - Chemical …, 2015 - pubs.rsc.org ... These wild-type proteins or their single mutant isoforms (pdb code: 3D53, 2F99, 1JSY, 1FHI(bearing a Q83E mutation), 1MEJ ... yellow sticks); (B) close-up view of the Cu1 binding site inCu·6-PGLac (PDB code 4TM7 ... The X-ray structure was refined to a resolution of 1.39 Å (Fig. ...
82 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 ...
83 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. ...
84 3d5t - Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures 2015 S Shokrollahzade, F Sharifi, A Vaseghi… - Journal of theoretical …, 2015 - Elsevier ... Mesophilic, Burkholderia pseudomallei, 3D5T/A, 2.51. ... Fig. 1. The structure ofadenylate kinases from the psychrophile Bacillus globisporus (PDB ID: 1S3G). ... Thestructure is shown as surface representation by Pymol software. ...
85 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. ...
86 3d64 - Crystallization and preliminary X-ray diffraction analysis of the S-adenosylhomocysteine hydrolase (SAHH) from Thermotoga maritima 2014 M He, Y Zheng, CH Huang, G Qian, X Xiao… - Structural Biology and …, 2014 - journals.iucr.org ... 17, 2134-2144.] ), Burkholderia pseudomallei (PDB entry 3d64 ; Seattle Structural GenomicsCenter for Infectious Disease, unpublished work), Trypanosoma ... This model was generated fromthe structure of Mycobacterium tuberculosis SAHH (PDB entry 3dhy ; 43 ...
87 3d64 - S-adenosyl-L-homocysteine hydrolase and methylation disorders: Yeast as a model system 2013 O Tehlivets, N Malanovic, M Visram… - … et Biophysica Acta (BBA …, 2013 - Elsevier ... 1. AdoMet — a principal methyl group donor and more. Beyond its role in protein synthesisand structure, methionine, after its activation to AdoMet by methionine adenosyltransferase,plays a crucial role in many aspects of cellular metabolism. ...
88 3d64 3glq, 3n58 An Inexpensive Method for Selecting Receptor Structures for Virtual Screening 2015 Z Huang, CF Wong - Journal of chemical information and , 2015 - ACS Publications ... SPI also performed better than the best docking energy, the molecular volume of thebound ligand, and the resolution of crystal structure in selecting good receptorstructures for virtual screening. The implications of these findings ...
89 3d64 3lls, 3qk8, 3ome, 3n58, 3oq8, 3myb, 3p5m, 3sll, 3i4e PEPTIDOMIMETIC COMPOUNDS 2015 RT Skerlj, AC Good - US Patent 20,150,353,606, 2015 - freepatentsonline.com ... TABLE 2. PDB ID, Key Cysteine residue. 3dp7, CYS10. 1nhw, CYS100. 1q51, CYS102. ... 1x9j,CYS227. 3n58, CYS231. 3d64, CYS238. 3ond, CYS244. ... In general the term helix or helicalis used to refer to any type of helical structure, including 3 10 -helices, -helices and -helices ...
90 3d64 3n58 An enzyme captured in two conformational states: crystal structure of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii 2015 T Manszewski, K Singh, B Imiolczyk - Section D: Biological , 2015 - scripts.iucr.org ... pseudomallei (Seattle Structural Genomics Center for Infectious Disease, unpublished work,PDB entry 3d64 ), Brucella melitensis (unpublished work, PDB entry 3n58 ... Here, we present thefirst crystal structure of SAHase from a nodulating bacterium, Bradyrhizobium ...
91 3d64 3n58 Crystal structures of S-adenosylhomocysteine hydrolase from the thermophilic bacterium Thermotoga maritima 2015 Y Zheng, CC Chen, TP Ko, X Xiao, Y Yang… - Journal of structural …, 2015 - Elsevier ... The Refseq or PDB numbers of these sequences are: T. maritima, AAC01562.1 ... 1B3R;Trypanosoma brucei, 3H9U; M. tuberculosis, 3DHY; B. melitensis, 3N58; B. pseudomallei, 3D64.The secondary structure elements (helices (α) and strands (β)) of tmSAHH are shown above ...
92 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, ...
93 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 ...
94 3dah - Crystal structure of E. coli PRPP synthetase 2019 W Zhou, A Tsai, DA Dattmore- Structural, 2019 - bmcstructbiol.biomedcentral.com Overall, this study details key structural features of an enzyme that catalyzes a critical step in nucleotide metabolism The structure was solved by molecular replacement using the PRPP synthetase from Burkholderia pseudomallei ( PDB 3DAH ) as the search model [14]
95 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 ...
96 3dah - Modeling of Protein Flexibility and Inter-Molecular Interactions: Applications to Computer-Aided Drug Design and Discovery 2012 R Ai - 2012 - escholarship.org ... Page 22. xxi Figure 5.1 .95 Summary of ligand binding capacity and subdomains of HSA using PDB structure 1E7E. Long-chain fatty acids are depicted in VDW representation using VMD 1.8.7. ...
97 3dah - Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase: a bent dimer defining the adenine specificity of the substrate ATP 2015 RW Andersen, LL Leggio, B Hove-Jensen, A Kadziola - Extremophiles, 2015 - Springer ... 1 3 structure of PRPP synthase of the thermophilic, metha- nogenic archaeon M. jannaschii istetrameric and appears to be built by two dimers ... 2007), and the Gram-negative Betaproteobacterium Burkholderia (Pseudomonas) pseudomallei (PDB code 3DAH) have hex ...
98 3dmo - Structural and functional analyses of< i> Mycobacterium tuberculosis Rv3315c</i>-encoded metal-dependent homotetrameric cytidine deaminase 2010 ZA S?nchez-Quitian, CZ Schneider, RG Ducati? - Journal of structural Biology, 2010 - Elsevier ... in the PDB (3IJF). Fig. 7A and B show two views of the canonical homotetrameric structure observed for CDAs from S. cerevisiae (1R5T), B. subtilis (1UX1, 1UWZ, 1UX0, 1JTK), Mus musculus (1ZAB, 2FR5, 2FR6), Bacillus anthracis (2D30), Burkholderia pseudomallei (3DMO), ...
99 3dmo 3mpz Análise bioquímica, estrutural e funcional da enzima citidina deaminase (EC 3.5. 4.5) de Mycobacterium tuberculosis H37Rv 2014 ZAS Quitian - 2014 - meriva.pucrs.br ... This work presents the crystal structures of MtCDA in complex with uridine (2.4 Å resolution) and ...process, showing that structural flexibility of some residues are important to product binding. ... MtCDAstructure. The role of the conserved glutamate-47 (E47) residue was ...
100 3dmo - Achievements of structural genomics 2011 TC Terwilliger - 2011 - permalink.lanl.gov ... Semi-automated Structure determination ~ ... PDB 3BV6, 2275 AA Metallo protein - ... l University ofIowa 2 University of Michigan Medical School Crystal structures of the FDTS-FAD- 3The JointCenter for Structural Genomics at GNF 4SSRL, Stanford University dUMP complex. ...
101 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 ...
102 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; ...
103 3dmo 3mpz Crystal structure determination and dynamic studies of< i> Mycobacterium tuberculosis</i> Cytidine deaminase in complex with products 2011 ZA S?nchez-Quitian, LFSM Timmers? - Archives of Biochemistry and Biophysics, 2011 - Elsevier ... Furthermore, in order to verify if these conformations are in agreement with CDA of different organism previously published, we analyzed other 13 CDA structures (PDB access codes: 3IJF, 3MPZ, 1MQ0, 3DMO, 1UX1, 2D30, 1UX0, 1UWZ, 1JTK, 2FR5, 1ZAB, 2FR6, and 3B8F) ...
104 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
105 3dmp - Unravelling the Potential of a New Uracil Phosphoribosyltransferase (UPRT) from Arabidopsis thaliana in Sensitizing HeLa Cells towards 5-Fluorouracil 2016 S Narayanan, P Sanpui, L Sahoo, SS Ghosh - International journal of , 2016 - Elsevier ... UPRT templates from Protein Data Bank (PDB) PDB: 2EHJ (E. coli UPRT), PDB: 3DMP(Burkholderia pseudomallei UPRT) and PDB: 1BD4 (Toxoplasma gondii UPRT) were chosenfor generating the three ... 1). The three-dimensional structure of AtUPRT ( Fig. ...
106 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
107 3dms - Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases 2012 R Vinekar, C Verma, I Ghosh - BMC , 2012 - bmcbioinformatics.biomedcentral. ... The current study therefore concentrates mainly on dimeric NADP-dependent IDHs from subfamilies I and II and additionally subfamily IV (Table 1), with an emphasis on regulation in dimeric M.tb IDH. Burcholderi apseudomallei BpIDH Q63WJ4_BURPS 3DMS. ...
108 3dms - Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase 2012 S Gon?alves, SP Miller, MA Carrondo, AM Dean? - Biochemistry, 2012 - ACS Publications ... To date, there are 27 crystal structures of E. coli isocitrate dehydrogenase in the Protein Data Bank (Table 3). Burkholderia pseudomallei Strain 1710b (UNIPROT Q3JV82), 74.2% identity 3dms 71 1.65 2011 0.92 0.62 ...
109 3dpi - Protein-protein interaction and molecular dynamics analysis for identification of novel inhibitors in Burkholderia cepacia GG4 2016 M Gupta, R Chauhan, Y Prasad, G Wadhwa - Biology and Chemistry, 2016 - Elsevier ... Homology based protein structure prediction employs submission of query protein sequenceto BLASTp against PDB database for identifying ... 3DPI, 2PZ8 and 1NSY. ... The dimensions of bindingspace on three dimensional structure of protein were identified in DockBlaster itself. ...
110 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 (
111 3e7d 3uk1 CH pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability 2014 M Kumar, PV Balaji - Journal of molecular modeling, 2014 - Springer ... The coordinates of proteins included in the dataset were downloaded from the protein databank [33]. ... discoideum non-muscle type myosin-2 heavy chain (PDB id 3BZ9). ... Brucella abortus CobH, precorrin-8X methylmutase 3E7D D Phe16:CE1 Tyr12 2.83 1.84 172 66 ...
112 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 ...
113 3ecd 3h7f A novel serine hydroxymethyltransferase from Arthrobacter nicotianae: characterization and improving catalytic efficiency by rational design 2014 W Jiang, L Chen, S Yuan, B Li, Z Liu - BMC biotechnology, 2014 - biomedcentral.com ... directed mutagenesis was indicated on the three-dimensional structure of AnSHMT, which wasconstructed from the known x-ray structure of Burkholderia Pseudomallei MycobacteriumTuberculosis T.Th.Hb8 (PDB entry 3H7F, 2DKJ and 3ECD) using Swiss ...
114 3ecd - Model the Solvent-Excluded Surface of 3D Protein Molecular Structures Using Geometric PDE-Based Level-Set Method 2009 Q Pan, XC Tai - Communications in Computational Physics, 2009 - uib.no ... where ? is a very small value and chosen to be O(?x). 3 Numerical implementation 3.1 Initial construction The data of the complex 3D protein molecular structures, saved as pdb format files, can be downloaded from the free website of the protein data bank: http://www.rcsb.org. ...
115 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. ...
116 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. ...
117 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 ...
118 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 ...
119 3eg4 3mdx, 3qxi, 3lqw, 3laa, 3oc7 Nouvelles méthodes de calcul pour la prédiction des interactions protéine-protéine au niveau structural 2015 P Popov - 2015 - theses.fr ... au niveau structural Thèse soutenue publiquement le « 28 Janvier 2015 », devant le jury composéde : ... blue, respectively). Right: native structure of Target 58 (grey) and medium-quality model pro- ...18 2.2 Query protocols for the PDB that were used to compose the bound bench- ...
120 3eg4 - Tetrahydrodipicolinate N-Succinyltransferase and Dihydrodipicolinate Synthase from Pseudomonas aeruginosa: Structure Analysis and Gene Deletion 2012 R Schnell, W Oehlmann, T Sandalova, Y Braun? - PloS one, 2012 - dx.plos.org ... In addition, the coordinates for DapD from Campylobacter jejuni (2RIJ), Enterococcus feacalis (3CJ8), Brucella melitensis (3EG4), and Yersinia ... model of the trimer of the putative tetrahydropyridine-2-carboxylate N-succinyltransferase from Campylobacter jejuni (PDB code ...
121 3eiy - Utilising Graph Machine Learning within Drug Discovery and Development 2020 T Gaudelet, B Day, AR Jamasb, J Soman- arXiv preprint arXiv, 2020 - arxiv.org and evolve along a temporal dimension resulting in changes to composition, structure and attributes One such approach is to use a graph's structural information to regularise embeddings authors suggest the atten- tion mechanism is decoupled from the architecture and should
122 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
123 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. ...
124 3eiz 3i4t High pKa variability of cysteine residues in structural databases and the effect of H-bond contributions 2014 SM Marino, İ Soylu - Türk Biyokimya Dergisi [Turkish Journal of …, 2014 - turkjbiochem.com ... High pKa variability of cysteine residues in structural ... RESULTS of ppka3 on PDB-crystal datasetprot=protein name res_num=residue number H-bond=hydrogen bond contribution to pKaprediction (pKa) Coul=electrostatics (from Coulombic interactions) contribution to pKa ...
125 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. ...
126 3ej0 3gqt In silico modeling of cooperative ligand binding 2011 M Vass - theop11.chem.elte.hu ... binding conformations of ligands. A set of 115 X-ray crystal structures was collected from the RCSB Protein Data Bank (PDB) containing at least two non-cofactor type ligands in close proximity to each other believed to be a result of cooperative binding. The commercial ...
127 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 ...
128 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
129 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
130 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
131 3ek1 - Conservation of water molecules in protein binding interfaces 2012 Z Li, Y He, L Cao, L Wong, J Li - International Journal of Bioinformatics Research and Applications, 2012 - Inderscience ... Figure 6 Water-contacting structure of four aligned alanine residues in: a rat formyltetrahydrofolate dehydrogenase subunit interface (a, [PDB:2O2P]), and three betaine aldehyde dehydrogenase subunit interfaces (b[PDB:2WOX], c[PDB:1WNB] and d[PDB:3EK1]). ...
132 3ek1 3i44 A computational integrating kinetic study on the flexible active site of human acetaldehyde dehydrogenase 1 2016 Y Xu, J Lee, HS Yang, ZR L, H Mu, JM Yang - Process , 2016 - Elsevier ... In the first step, binding pocket residues were calculated based on the 3D structure of ALDH1via the Pck pocket ... We found 25 template PDB structures (1a4s, 1bxs, 1euh, 1o04, 1t90, 1uxt,1uzb, 1wnd, 2d4e, 2imp, 2j6l, 2o2p, 2ve5, 2w8n, 3b4w, 3ed6, 3ek1, 3i44, 3ifg, 3jz4 ...
133 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 ...
134 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 ...
135 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 ...
136 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: ...
137 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
138 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 ...
139 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 ...
140 3ek2 - Crystalline Structure of FABI from Burkholderia Pseudomallei 2017 NR Krishnamurthy - US Patent , 2017 - freepatentsonline.com ... Analysis of X-Ray Structure of BpmFabI. ... The structural superposition showed an rms deviationof 1.047 , 0.87 and 1.07 respectively for Bpm (256 Ca atoms; PDB; 3EK2), Ec (251 Caatoms; PDB; 4JQC) and ScFabI (242 Ca atoms; PDB; 4FS3) crystal structures. ...
141 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. ...
142 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 ...
143 3ek2 - Paclitaxel Induces Apoptosis in Breast Cancer Cells through Different Calcium-Regulating Mechanisms Depending on External Calcium Conditions 2014 Z Pan, A Avila, L Gollahon - International journal of molecular sciences, 2014 - mdpi.com ... 3 2i6x ?10.3 Porphyromonas gingivalis hydrolase 4 3ek2 ?10.3 Burkholderia pseudomallei eonyl reductase ... Two libraries, ?pdb_subset.py? and ?pdb_centermass.py? from the pdb-tools project (https://code.google.com/p/pdb-tools/) were modified and used in Artemis. ...
144 3ek2 - Structure-based drug design on the enoyl-ACP reductases of Yersinia pestis and Burkholderia pseudomallei 2012 MW Hirschbeck - opus.uni-wuerzburg.de ... In the PDB database an apo structure of BpFabI had already been deposited (PDB code 3EK2), which was crystallized in 10% PEG 6000 and 100 mM HEPES pH 7.0. ...
145 3ek2 - Pyridone FabI Inhibitors and Uses Thereof 2016 P Tonge - US Patent App. 15/130,365, 2016 - Google Patents ... Selected residues of the saFabI-NADPH-PT173 structure (gray, subunit F) and the centralhydrogen ... Structural differences between diphenyl ether and pyridone ternary complexes. ... residueroot mean square deviation (RMSD) values between the triclosan-bound (PDB code 4ALI ...
146 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 ...
147 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; ...
148 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 ...
149 3enk - Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum 2019 YW Nam, M Nishimoto, T Arakawa, M Kitaoka- Scientific reports, 2019 - nature.com Here, we focused on structural features of GalE from B. longum JCM1217 (bGalE) The main chain structure of bGalE is similar to those of bacterial and eukaryotic GalEs. C RMSD values (distance cutoff = 2.0 ) of the UDP-GlcNAc complex with hGalE ( PDB ID 1HZJ, ... We built a reliable homology model of BLLJ_1592 (GQME = 0.72 and QMEAN = −2.34) using the SWISS-MODEL server45 with an unpublished structure of GalE from Burkholderia pseudomallei (PDB ID: 3ENK, sequence identity = 42.3%) as a template
150 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 ...
151 3enk - Highly selective l-threonine 3-dehydrogenase from< i> Cupriavidus necator</i> and its use in determination of l-threonine 2011 T Ueatrongchit, Y Asano - Analytical Biochemistry, 2011 - Elsevier ... BaGluE, UDP-glucose 4-epimerase from Bacillus anthracis (2C20); BpGluE, UDP-glucose 4-epimerase from Burkholderia pseudomallei (3ENK); SvDHT, DTDP-glucose 4,6-dehydratase from Streptomyces venezuelae (1R66); ...
152 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. ...
153 3enk - Structure and in silico substrate-binding mode of ADP-L-glycero-D-manno-heptose 6-epimerase from Burkholderia thailandensis 2013 MS Kim, A Lim, SW Yang, J Park, D Lee? - Acta Crystallographica Section D Biological Crystallography, 2013 - scripts.iucr.org ... complexed with six different types of substrate have been deposited in the Protein Data Bank (Table 2 ... Cov ++ (%), Cavity volume (? 3 ), Molecular volume (? 3 ), Cavity/molecule, RelatedPDB entries. ... B. pseudomallei (3enk ), UDP- -D-glucose, 7.13, 2.72, 22, 37, 93, 830.8, 181.5, ...
154 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)...
155 3enk - UDP-galactose 4′-epimerase from the liver fluke, Fasciola hepatica: biochemical characterization of the enzyme and identification of inhibitors 2014 VL ZINSSER, S LINDERT, S BANFORD… - …, 2014 - Cambridge Univ Press ... These results demonstrate that, despite the structural and biochemical similarities of FhGALEand HsGALE, it is possible to discover compounds which preferentially inhibit ... pymol.org) to thesubunits of Burkholderia pseudo- mallei GALE structure (PDB ID: 3ENK) and NAD+ ...
156 3eol - Filogenia molecular das enzimas isocitrato liase e malato sintase e sua evoluo em Viridiplanta 2014 RVM Almeida - 2014 - repositorio.ufrn.br ... Bayesian analysis). The identification of structural patterns in the evolution of theenzymes was made through homology modeling and structure prediction from proteinsequences. Based on comparative analyzes of in silico ...
157 3eom 3pfd, 3swo, 4n5f 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA … 2015 M Schürmann, R Meijers, TR Schneider… - … Section D: Biological …, 2015 - scripts.iucr.org ... (2011). Acta Cryst. D67, 235-242.] ) with the crystal structure of an acyl-CoAdehydrogenase from Thermus thermophilus HB8 (PDB entry 1ukw ; RIKEN StructuralGenomics/Proteomics Initiative, unpublished work) as the search model. ...
158 3eon - Update 1 of: Proteases universally recognize beta strands in their active sites 2011 PK Madala, JDA Tyndall, T Nall, DP Fairlie - Chemical Reviews, 2011 - ACS Publications ... All endoprotease complexes deposited in the Protein Data Bank (PDB http://www.rcsb.org/pdb mir- rored at http://oca.wehi.edu.au:8383/oca/22) through July 2009 were included in this study, updated with only a few key structures beyond that date. ...
159 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 ...
160 3eoo - Design, Synthesis and Evaluation of Pyrazolo-Pyrazole Derivatives onMethylisocitratelyase Of Pseudomonas aeruginosa: Insilico and invitro study 2016 M Pulaganti, C Suresh Kumar - Journal of Biomolecular Structure , 2016 - Taylor & Francis ... possessing the highest sequence identity. We finally picked the A-chain of 1MUM and 3EOOas ... carefully editing PIR file and PDB file template.The developed .ali, .py, pdb template files ...structure of MICL with build command of modeller, using default parameters. ...
161 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. ...
162 3eoo - Massenspektrometrische Untersuchungen zur Struktur der Peroxisom-Proliferator-aktivierten Rezeptoren- und-/ 2017 R Schwarz - 2017 - opendata.uni-halle.de Optische Dichte bei 600 nm PAGE Polyacrylamid-Gelelektrophorese PBP PPAR Binding Protein PCR Polymerase-Kettenreaktion PDB Proteindatenbank PflB Pyruvate Formate Lyase PMSF Phenylmethansulfonylfluorid PPAR Peroxisom-Proliferator-aktiverter Rezeptor ppm ... Die umfangreichsten Röntgenkristallstrukturen wurden mit dem Subtyp PPAR-γ (PDBEinträge: 3DZU, 3DZY und 3EOO) gewonnen, in denen das Volllängenprotein ohne den flexiblen N-Terminus mit RXR-α und verschiedenen Liganden und Kofaktoren kokristallisier
163 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 ...
164 3ezn - Mechanism of Dephosphorylation of Glucosyl-3-phosphoglycerate by a Histidine Phosphatase 2014 Q Zheng, D Jiang, W Zhang, Q Zhang, Q Zhao - Journal of Biological Chemistry, 2014 - ASBMB ... 2B). Other significant structural matches included phosphoserine phosphatase 1 (34) (PsP1; Protein Data Bank code 4IJ5) and phosphoglycerate mutase (35) (PGM; Protein Data Bank code 3EZN). ... PDB, Protein Data Bank. ...
165 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). ...
166 3f0d - Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins 2020 M Macchiagodena, M Pagliai, C Andreini, A Rosato- ACS, 2020 - ACS Publications Journal Logo. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. Marina Macchiagodena Marina Macchiagodena. Dipartimento di
167 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 .... ...
168 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 ?. ...
169 3f0g 3ieq Structural studies to inform antimicrobial drug discovery and the basis of immunity against T6 effectors 2013 P O'Rourke - 2013 - discovery.dundee.ac.uk ... Search models for molecular replacement used coordinates from orthologues in E. coli (PDB code: 1GX1; ~33% identity, Kemp et al., 2002) and B.pseudomallei (PDB code: 3F0G;63%,Begley et al., 2011) for PfIspF and BcIspF respectively, edited to remove all non-protein atoms. ...
170 3f9i - Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2 S, 3 R, 4 S)-4-hydroxyisoleucine with three asymmetric centers 2017 X Shi, T Miyakawa, A Nakamura, F Hou, M Hibi- Scientific reports, 2017 - nature.com The structure of HILDH-NADH was determined using the molecular replacement method performed by the program MOLREP on the CCP4 suite using the structure of 3-ketoacyl-(acyl-carrier-protein) reductase (PDB code, 3F9I; sequence identity, 34%) as the initial model.
171 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
172 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 ...
173 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 ...
174 3fdz - Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation 2013 T Hitosugi, L Zhou, J Fan, S Elf, L Zhang, J Xie? - Nature Communications, 2013 - nature.com ... (a) Cartoon representation of 2,3-BPG location from structure 3FDZ superposed on PGAM1 (PDB accession code: 1YFK). H11 and Y92 are directly proximal to and Y26 is also close to cofactor (2,3-BPG)/substrate (3-PG) binding site. ...
175 3fdz - Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth 2017 Y Wang, WS Cai, L Chen, G Wang - Oncotarget, 2017 - ncbi.nlm.nih.gov ... We then used the crystal structure ( PDB ID: 3FDZ ) as the reference to study the structural deviations of S 0 wt and S 1 phos, because the crystal structure had recorded faithfully the actual binding of 2,3-BPG with PGAM1. ...
176 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. ...
177 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). ...
178 3fs2 - In silico quest for putative drug targets in Helicobacter pylori HPAG1: molecular modeling of candidate enzymes from lipopolysaccharide biosynthesis pathway 2012 M Sarkar, L Maganti, N Ghoshal, C Dutta - Journal of molecular modeling, 2012 - Springer ... Fig. 7 Sequence alignment of 2-dehydro-3-deoxyphosphoocto- nate aldolase of H. pylori HPAG1 with template proteins from Aquifex aeolicus (PDB id: 1fx6), Haemophilus influenza (PDB id: 1o60) and Brucella melitensis (PDB id: 3fs2). ...
179 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. ...
180 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). ...
181 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: ...
182 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 ...
183 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 ...
184 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 ...
185 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 ...
186 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 ...
187 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. ...
188 3fvb - Catalysis of iron core formation in Escherichia coli bacterioferritin 2009 S Wong - 2009 - circle.ubc.ca ... Another example of a small molecule occupying a ferroxidase pore was recently discovered through crystallographic analysis of BFR from Brucella melitensis (PDB ID: 3FVB). This structure revealed imidazole bound to iron at the ferroxidase site such that the imidazole is located in the ferroxidase pore directly between the ferroxidase site and the pore opening. ...
189 3fvb - I. Synthesis Of Anthraquinone Derivatives For Electron Transfer Studies In DNA. II. Characterization Of The Interaction Between Heme And Proteins. 2011 Y Cao - 2011 - scholarworks.gsu.edu ... 64 Figure 3.2 (A) The active site of HSA (PDB ID 1N5U); Lys190 is in blue; (B) The active site of Mb (1WLA); Lys45 and Lys96 are in blue. ... (A) The IsdA (PDB ID: 2ITF) binding pocket; (B) the IsdC (PDB ID: 2O6P) binding pocket; (C) the Shp (PDB ID: 2Q7A) ...
190 3gaf - Sequence and structural studies of proteins associated with cell wall biosynthesis lipolysis and isoniazid drug resistance in Mycobacterium tuberculosis 2018 S Anishetty - 2018 - baadalsg.inflibnet.ac.in Page 4. 63 of recognizing the native structure out of decoy structures 3D coordinates of Isoniazid-NAD adduct ( PDB : 2IDZ) and Triclosan ( PDB : 3OID) was obtained from PDB Rv0547c Oxidoreductase 5e-35 20% FX6-K - Rv0927c Oxidoreductase 1e-32 23% FX6-K 3GAF 41.32
191 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 ...
192 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 ...
193 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 ...
194 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 ...
195 3gbz - How evolution designs functional free energy landscapes of proteins? A case study on emergence of regulation in CDK family kinases. 2020 Z Shamsi, D Shukla- Molecular Systems Design & Engineering, 2020 - pubs.rsc.org structures of CDK2 ( PDB ID: 5OSM, 6Q3F, 6Q4A, 6Q4B, 6Q4C, 6Q4D, 6Q4K), G/CDK ( PDB ID: 3GBZ ), and pfpk5 structures are native-like based on GA341 score and have comparable DOPE score with CDK2 native structure as shown in PDB ID for CMGI for native CDK2 score
196 3gbz - How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase family 2020 Z Shamsi, D Shukla- Molecular Systems Design & Engineering, 2020 - pubs.rsc.org PDB ID: 5OSM, 6Q3F, 6Q4A, 6Q4B, 6Q4C, 6Q4D, 6Q4K), G/CDK ( PDB ID: 3GBZ ), and pfpk5 on the GA341 score and have comparable DOPE scores with the CDK2 native structure as shown Template's PDB ID, DOPE score for CMGI, DOPE score for native CDK2, GA341 score
197 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. ...
198 3ge4 - Relation between molecular shape and the morphology of self-assembling aggregates: a simulation study 2011 R V?cha, D Frenkel - Biophysical journal, 2011 - Elsevier Supporting Material Figure2.: A cut through the middle of a protein vesicle formed as bilayer of alpha-helices (3GE4 in Protein Database), where alpha-helices are visualised as rods and unstructured loops as wires
199 3gka - Crystal Structure Determination and Mutagenesis Analysis of the Ene Reductase NCR 2012 S Reich, HW Hoeffken, B Rosche, BM Nestl? - ChemBioChem, 2012 - Wiley Online Library ... Figure 1. Crystal structure of the ene reductase NCR (PDB ID: 4A3U) dis- played in cartoon representation and showing prosthetic ... in the Supporting Infor- mation), 12-oxophytodienoate reductases 1 and 3 (OPR1 and OPR3) and N-ethylmaleimidine reductase (3GKA) from the ...
200 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, ...
201 3gka - Estudo estrutural das enzimas Topoisomerase II Mitocondrial e Old Yellow Enzyme de Trypanosoma cruzi 2014 NC Rodrigues - teses.usp.br ... resolution of 1.27 and 2.00 , respectively. The atomic coordinates and structure factors of the TcOYE structure in P212121 and P21 crystalline forms have been deposited in the Protein DataBank with the accession codes 4E2B and 4E2D, respectively. TcOYE displays a ...
202 3gka - Two new ene-reductases from photosynthetic extremophiles enlarge the panel of old yellow enzymes: CtOYE and GsOYE 2020 MS Robescu, M Niero, M Hall, L Cendron- Applied Microbiology, 2020 - Springer The most peculiar structural features of each enzyme are depicted in bright orange (loop 3 In the active site of GsOYE structure , a chloride anion, present in the crystallization In the structures of the GsOYE complexes, both para-hydroxybenzaldehyde (pHBA; PDB : 6S31) (Fig
203 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 ...
204 3gka - Structural studies of the< i> Trypanosoma cruzi</i> Old Yellow Enzyme: Insights into enzyme dynamics and specificity 2013 MT Murakami, NC Rodrigues, LM Gava? - Biophysical Chemistry, 2013 - Elsevier ... of the TcOYE structure in P2 1 2 1 2 1 and P2 1 crystalline forms have been deposited in the Protein Data Bank with the ... ? rmsd over 348 C? atoms - PDB code: 2GOU) and Burkholderia pseudomallei (BpOYE - 1.24 ? rmsd over 341 C? atoms - PDB code: 3GKA) revealed a ...
205 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
206 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 ...
207 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). ...
208 3glq - Functional Prediction of Binding Pockets 2012 M Kontoyianni, CB Rosnick - Journal of chemical information and modeling, 2012 - ACS Publications ... The dataset was compiled using the protein databank, the Structural Classification of Proteins (SCOP),68 the Enzyme Classification (EC)69 system and the Washington University Basic Local Alignment Search Tool Version 2.0 (WU- ...
209 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 ...
210 3glq - Inexpensive method for selecting receptor structures for virtual screening 2015 Z Huang, CF Wong - Journal of chemical information and modeling, 2015 - or.nsfc.gov.cn ... 1LI4, 1V8B, 1XWF, 2H5L, 2ZIZ, 2ZJ0, 2ZJ1, 3CE6, 3D64b, 3DHY, 3G1U, 3GLQ, 3H9U, 3N58 ...the results for docking 152 actives and 9942 decoys to 36 crystal structures for BRAF. For thissystem, the SPI identified the best structure (PDB id 3IDP) for virtual screening as the other ...
211 3gmt - Exploring protein dynamics using graph theory and single-molecule spectroscopy 2017 R Peach - 2017 - spiral.imperial.ac.uk 4.1 Weighted graph construction from an experimental PDB structure The increased understanding between structure , dynamics and function offers opportunities for protein ... Despite the myriad of structures, only four are available in the apo state (PDB ID: 4AKE, 2RH5, 3UMF and 3GMT) which takes the form of the open conformation.
212 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. ...
213 3gmt - Approaches for studying allostery using network theory 2018 M Hodges - 2018 - spiral.imperial.ac.uk 101 6.9 Optimization of coherent active and allosteric site motion in 3-dimensional structure . . . 102 B.1 DBSCANmethodforclustering a structural basis for allostery based on comparisons of active and inactive structures . The concept of struc
214 3gmt - Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins 2017 SL Seyler - 2017 - search.proquest.com The intricacies of the current state of knowledge surrounding protein conformational. transitions and the structure -function connection is perhaps more easily understood in the and four in ligand-free (apo), open-like states ( PDB IDs 4ake, 2rh5, 3umf, 3gmt [26])
215 3gmt - Adenylate kinase from< i> Streptococcus pneumoniae</i> is essential for growth through its catalytic activity 2014 TT Thach, TT Luong, S Lee, DK Rhee - FEBS Open Bio, 2014 - Elsevier ... Open, ligand-free SpAdK structure was solved by molecular replacement using PHENIX [35] with AdK from Marinibacillus marinus (PDB ID: 3FB4) and Burkholderia pseudomallei (PDB ID: 3GMT) as search models. ...
216 3gmt - Sampling large conformational transitions: adenylate kinase as a testing ground 2014 SL Seyler, O Beckstein - Molecular Simulation, 2014 - Taylor & Francis Out of these structures only four (PDB IDs 4ake, 2rh5, 3umf, 3gmt) were crystallised in the apo form, i.e. in the absence of a substrate-like ligand, and these structures represent the open conformations of AdK.
217 3gmt - Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations 2013 TP Schrank, JO Wrabl, VJ Hilser - Dynamics in Enzyme Catalysis: Topics in Current Chemistry, 2013 - Springer ... PDB structures 1AK2, 1E4V, 2AR7, 2RH5, 2XB4, 3GMT, 3NDP, each pairwise superimposed on 4AKE, the AK(e) structure are displayed. ... All adenylate kinase structures were retrieved from the Protein Data Bank (PDB) [71]. ...
218 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 ...
219 3gp5 - Vanadate in structural biology 2014 S Akabayov, B Akabayov - Inorganica Chimica Acta, 2014 - Elsevier ... Protein data bank; Data mining; Protein-vanadate complex. ... Structures of biological macromolecules containing ligands with vanadium were downloaded from the Protein Databank (www.pdb.org ... PDB, ProteinOrganism, CLASS a, Geometry b, DNA/RNA c, Metal Ion d, TS e, Ligand ...
220 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. ...
221 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
222 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. ...
223 3grk 3s55, 4eit, 3tzq, 4j07 Crosslinked helix dimers as versatile scaffolds for mimicking topologically complex epitopes 2018 MG Wuo - 2018 - search.proquest.com 1 1.2 Surface architecture variation among PPIs affect ligandability ..... 3 aliphatic core but lacks any heptad repeat structure and knob/hole packing orientation. ( PDB Codes: 1LLM, 1TMX, 3V3E) .... 57
224 3grk - Expression und Mutagenese von VEP1-kodierten Progesteron-5β-Reduktasen aus pharmazeutisch interessanten Angiospermen 2012 P Bauer - 2012 - opus4.kobv.de ... Parallel wurden mit Hilfe der „Superposition“-Funktion der Wincoot Software (II.2.5) in silico die Cosubstrat-Bindetasche der DlP5βR jeweils mit der von verschiedenen NADHabhängigen SDR-Enzymen überlagert (PDB: 2ztl, 3d3w, 3grk,..
225 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]. ...
226 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
227 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 ...
228 3gtd 3qbp, 3rrp Structural and functional characterization of Trypanosoma cruzi fumarate hydratase isoforms 2014 RAP de Pdua - teses.usp.br ... TcFHs structural models, built by homology modeling using the Leishmania major fumarase crystalstructure as template, were compared to ... Keywords: fumarase, fumarate hydratase, Chagas disease,selective inhibitors, crystal structure. ... The fainter structures correspond to the ...
229 3gvc - Improved xylitol production by expressing a novel D-arabitol dehydrogenase from isolated Gluconobacter sp. JX-05 and co-biotransformation of whole cells 2017 X Qi, H Zhang, TA Magocha, Y An, J Yun, M Yang - Bioresource , 2017 - Elsevier ... Phyre2 (Kelley et al., 2015) was used to predict the 3D structure of ArDH. ..Another two SDR enzymes, short-chain dehydrogenase reductase (PDB ID: 3GVC) of M. tuberculosis and galactitol dehydrogenase (PDB ID: 2WSB) of R. sphaeroides were also used in the superposition of structure modeling. ...
230 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 ...
231 3gvg - Crystal structures of triosephosphate isomerase from methicillin resistant< i> Staphylococcus aureus</i> MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop 2012 S Mukherjee, A Roychowdhury, D Dutta, AK Das - Biochimie, 2012 - Elsevier ... Structural homologues to SaTIM in PDB were searched by the BLASTP server [46 ... sequence alignment of amino acid residues of SaTIM (3M9Y) with TIM from Bacillus stearothermophilus (2BTM), Thermotoga maritima (1B9B), Mycobacterium tuberculosis (3GVG), Vibrio marinus ...
232 3gvg 3kxq Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding 2013 Z Li, Y He, Q Liu, L Zhao, L Wong - BMC , 2013 - bmcbioinformatics.biomedcentral. ... Domain. PDB. Organism. Resolution (). #Water. #Atoms. ... 1.162. 0.680. 3GVG. M. tuberculosis.1.55. 41. ... Once the aligned wild type and mutant structures are obtained, the 25 water moleculesin wild type are searched in the mutant structure to determine whether it reappears or not ...
233 3gvg - Triosephosphate isomerase: a highly evolved biocatalyst 2010 RK Wierenga, EG Kapetaniou, R Venkatesan - Cellular and molecular life Sciences, 2010 - Springer ... 1AW2 M. marina No SO4 Dimer 2.65 20.0 21.9 3GVG M. tuberculosis No Dimer 1.55 14.5 16.9 1R2R O. cuniculus No Dimer 1.5 16.1 19.0 ... 3967 Page 8. Table 1 continued pdb code Source Mutant Active site ligand Oligomeric state Resolution (A? ) Rcryst (%) Rfree (%) ...
234 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 ...
235 3gvg - How proteins work 2011 M Williamson - 2011 - books.google.com ... in structure motifs 24 Membrane proteins are different from globular proteins 29 The structureofa protein is (more or less) determined by its sequence 31 Some proteins form metastablestructures 32 Structure is conserved more than sequence 33 Structural homology can be ...
236 3gvg - Structural and functional characterization of Mycobacterium tuberculosis triosephosphate isomerase 2011 SE Connor, GC Capodagli, MK Deaton? - Acta Crystallographica Section D Biological Crystallography, 2011 - scripts.iucr.org ... Anal. Biochem. 182, 319-326.] ). Initial crystallization conditions for MtTPI were obtained from the MtTPI-GOL structure deposited in the RCSB (PDB entry 3gvg ; Seattle Structural Genomics Center for Infectious Disease, unpublished work). ...
237 3gvg 4g1k Production, characterization and structural analysis of proteins from Corynebacterium pseudotuberculosis and snake venoms 2015 R Masood - 2015 - repositorio.unesp.br ... Structural alignment among different TIMs (3TA6, 3GVG, 1YYA, 1B9B, 4G1K and 2BTM) indicate that they are very similar to each other (Fig. 19). Alignment of C. pseudotuberculosis TIM with TIM (PDB code 3TA6) from Mycobacterium tuberculosis shows a very slight difference in the loop region as shown in the figure 19 A as they share 67% sequence identity and 0.4 RMSD value. . ...
238 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
239 3gvh - Analysis of the Mycoplasma bovis lactate dehydrogenase reveals typical enzymatic activity despite the presence of an atypical catalytic site motif 2018 Y Masukagami, KA Tivendale- , 2018 - mic.microbiologyresearch.org between MBOVPG45_0326 and the other bac- terial LDHs, and 2230 % identity across the region of align- ment between MBOVPG45_0326 and the other bacterial and parasitic MDHs in the PDB protein structure database 3GVH RCSB PDB Brucella melitensis LDH
240 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
241 3gvi - An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors 2016 P Laurino, Tth-Petrczy, R Meana-Paeda, W Lin - PLoS Biol, 2016 - journals.plos.org ... PDB (Protein Data Bank) IDs and corresponding cofactors: 1JG2, ADN; 3GVI, ADP; 2HMU, ATP;2XXB, AMP; 1BWC, FAD; 1V5E, FAD; 1EG2, MTA; 2A14, 2PBF ... A) Zoom-in view of the structureof L-3-hydroxyacyl-CoA dehydrogenase belonging to the Rossmann fold (PDB 1F17 ...
242 3gvi - Rhizobitoxine enhances nodulation by inhibiting ethylene synthesis of bradyrhizobium elkanii from lespedeza species: validation by homology modelling and 2013 R Vijayan, P Palaniappan, SA Tongmin - World J of pharm and , 2013 - wjpps.com ... docking studies with the known inhibitor rhizobitoxine. The crystal structure of protein was taken from the Protein Data Bank (entry PDB code: 3GVI). So, we considered the active site residues predicted from the LIGSITE and CASTp has been used for binding with ...
243 3gwc - Similarity in the Amino Acid Sequences of Mycobacterium tuberculosis Protein Targets Involved in Binding Sites of Docking with Thiacetazone 2016 M Mafakheri, S Sardari- Pharm Anal Acta, 2016 - pdfs.semanticscholar.org reviewed and well known M. tuberculosis protein target was chosen (Table 1) then they were downloaded in pdb format from 68 3GWC Transferase -6.24 RRRHHHHM 21. A Structural View of Biology, An Information Portal to 124286 Biological Macromolecular Structures . 22
244 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
245 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.
246 3gwc 4emd, 4fkx, 4f4a PROTEIN-LIGAND INTERACTIONS AND STRUCTURE-BASED INHIBITOR DISCOVERY 2018 S Usha, S Selvaraj - 2018 - 14.139.186.108 i) Target structure A target structure experimentally determined through X-ray crystallography or NMR spectroscopy techniques and deposited in the PDB is the ideal starting point for docking. Structural genomics has accelerated the rate at which target structures are
247 3gwc - Virtual Screening of Novel Potent Molecules Targeting enoyl-ACP reductase as Antitubercular Agents by Molecular Docking studies 2019 V Shivakumar, PM Ramsana, M Risfa- Journal of, 2019 - search.proquest.com Fig 2. Structure and portions nomenclature of linezolid V. Shivakumar et al /J. Pharm. Sci. & Res NO. PDB ID RESOLUTION ENZYMES YEAR 1 2AF6 2.01 Trymidylate synthase 2005 2 2X23 1.80 enoyl-ACP reductase 2010 3 3GWC 1.9 Trymidylate synthase 2009
248 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 ...
249 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 ...
250 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 ...
251 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
252 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 ...
253 3h7f - Combinatorial Designing of Novel Lead Molecules Towards the Putative Drug Targets of Extreme Drug-Resistant Mycobacterium tuberculosis: A Future Insight for 2019 N Bachappanavar, S Skariyachan- Essentials of Bioinformatics, Volume II, 2019 - Springer glyoxylate and dicarboxylate. The native structure of serine hydroxymethyltransferase ( PDB ID: 3H7F ) possessed two chains (A and B) with molecular weight of 95226.08 Da and a resolution of 1.5 (R-value free, 0.196) (Fig. 12.2a). Further
254 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...
255 3h81 - Genomics-based discovery and engineering of biocatalysts for conversion of amines 2017 MM Heberling, CP Postema, TJ Meijer, M Otzen - rug.nl peptides and macrolactam polyketides through de novo biosynthesis [1,2]. The structural diversity and The structure of -Val (or other dialkylglycines) restricts the diversity of feasible ID) and an enoyl-CoA hydratase from Mycobacterium tuberculosis ( PDB : 3H81 , 62%), as seen
256 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
257 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
258 3h81 3myb Pseudomonas aeruginosa Isohexenyl Glutaconyl-CoA Hydratase (AtuE) Is Upregulated in Citronellate-grown Cells and Belongs to the Crotonase Family 2015 N Poudel, J Pfannstiel, O Simon, N Walter… - Applied and …, 2015 - Am Soc Microbiol ... Initial phases were obtained with 223 molecular replacement using PHASER (21). Two searchmodels were constructed 224 (PDB accession code: 3H81, 37.0% seq. ... The stereochemistry 235of the structure was validated with MOLPROBITY (24) and various tools in COOT. ...
259 3h81 3myb The Pseudomonas aeruginosa Isohexenyl Glutaconyl Coenzyme A Hydratase (AtuE) Is Upregulated in Citronellate-Grown Cells and Belongs to the Crotonase Family 2015 N Poudel, J Pfannstiel, O Simon, N Walter - Applied and , 2015 - Am Soc Microbiol ... models were constructed (one with the structure with PDB accession number 3H81 [sequenceidentity, 37.0%] and one with the structure with PDB accession number ... The stereochemistry ofthe structure was validated with the MOLPROBITY program (24) and various ...
260 3h81 4f47, 3rsi, 3r9s, 3r9t, 3oc7 Sequence analysis and structure prediction of enoyl-CoA hydratase from< i> Avicennia marina</i>: Implication of various amino acid residues on substrate–enzyme interactions 2013 U Jabeen, A Salim - Phytochemistry, 2013 - Elsevier ... Appendix A. Supplementary data. ...The second clade has many subdivisions. Enoyl-CoA hydratases in this clade belonged to Bacillus anthracis (3KQF, 3PEA), Geobacillus kaustophilus (2PBP), Mycobacterium tuberculosis (3PZK, 3H81, 3Q0J), Rattus norvegicus (1EY3, 1MJ3, 1DUB, 1DCI), Homo sapiens (2HW5, 2VRE), Escherichia coli K-12 (4FZW), Mycobacterium abscessus (3RSI) ...
261 3h81 3njd, 3qk8, 3qka, 3q1t, 3pe8, 3p85, 3p5m, 3ome, 3oc7, 3myb, 3moy, 3he2 Computational studies of enzyme function and dynamics 2012 P Yin - 2012 - iris.lib.neu.edu ... Page 20. 19 List of Abbreviations Abbreviation Meaning CSA Catalytic Site Atlas PDB Protein Data Bank THEMATICS Theoretical Microscopic Titration Curves POOL Partial Order Optimal Likelihood ? Angstr?ms ?C Degrees Celsius ESR Electron Spin Resonance NMR ...
262 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 ...
263 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 ...
264 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
265 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. ...
266 3hhe 3uw1 Structural modeling and docking studies of ribose 5-phosphate isomerase from Leishmania major and Homo sapiens: A comparative analysis for Leishmaniasis … 2015 PVSZ Capriles, LPR Baptista, IA Guedes… - Journal of Molecular …, 2015 - Elsevier ... identity: 42%); (iii) 2F8M [29], the R5PI type A structure from Plasmodium falciparum (identity:35%) and (iv) 3HHE [30], the R5PI type A structure from Bartonella ... The alignment analyses showedthat no PDB sequence was able to align against the 20 C-terminal amino acids ...
267 3hhe 3uw1 Biochemical and structural insights into an Ochrobactrum sp. CSL1 ribose-5-phosphate isomerase A and its roles in isomerization of rare sugars 2020 X Ju, X Xu, M Shen, X Mo, H Fan, L Liangzhi- Enzyme and Microbial, 2020 - Elsevier thermophilus (TtRpiA, 1UJ5), Burkholderia thailandensis (BtRpiA, 3UW1), Bartonella henselae (BhRpiA, 3HHE ) and E. coli (EcRpiA, 1O8B) with ligand-binding structures in PDB , the sequence Homology modeling is an option to investigate the structure -activity relationship of
268 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. ...
269 3hhe - In silico identification of inhibitors of ribose 5-phosphate isomerase from Trypanosoma cruzi using ligand and structure based approaches 2017 V de VC Sinatti, LPR Baptista, M Alves-Ferreira - Journal of Molecular , 2017 - Elsevier ... Abbreviations: LB, Ligand-Based pharmacophore hypothesis; SB, Structure -Based pharmacophore hypothesis. ... bound to R5P substrate ( PDB ID: 3K7S) and bound to the 4PEH ( PDB ID: 3K8C) [12 ... as query and the 1XTZ (identity of 46%), 1LK7 (identity of 42%), 3HHE (identity ...
270 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.
271 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]. ...
272 3hhj 4dyw Asociacin de genes nudA y htrA de Helicobacter pylori con severidad de patologas gstricas, estudio bioinformtico de la protena NudA. 2019 PA Lincoir Campos - 2019 - repositorio.udec.cl Page 1. Universidad de Concepcin Direccin de Postgrado Facultad de Ciencias Biolgicas - Programa de Magister en Ciencias con Mencin en Microbiologa Asociacin de genes nudA y htrA de Helicobacter pylori con severidad de patologas gstricas
273 3hhj - Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base 2010 T Nakamura, S Meshitsuka, S Kitagawa, N Abe? - Journal of Biological Chemistry, 2010 - ASBMB ... ?, Z = 19.0) and with dGTP (BdRppH-dGTP, 3EF5, rmsd = 1.9 ?, Z = 18.3) (40) and unknown proteins from Bartonella henselae (3HHJ, rmsd = 1.8 ... ray and NMR structures in the ligand-free form and 3.5 ?for 127 C? atoms between structures in the complex form (PDB IDs: 1MUT ...
274 3hja - Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus 2014 R Nagarajan, K Ponnuraj - Acta Crystallographica Section F: , 2014 - scripts.iucr.org ... 246, 511-521.] ), Borrelia burgdorferi (PDB entry 3hja ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and E. coli (PDB entry 1s7c ; Berkeley Structural Genomics Center, unpublished work) and fungal species as Saccharomyces cerevisiae (PDB ...
275 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. ...
276 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
277 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
278 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). ...
279 3hwi - Crystal structure of YnjE from Escherichia coli, a sulfurtransferase with three rhodanese domains 2009 P H?nzelmann, JU Dahl, J Kuper, A Urban? - Protein Science, 2009 - Wiley Online Library ... The tandem-domain rhodaneses from Thermus thermophilus (PDB entry 1uar), Mycobacterium tuberculosis (PDB entry 3hwi), Azotobacter vinelandii (Av_RhdA, PDB entry 1e0c) and Bos taurus (Rhodbov, PDB entry 1boi) with Z-scores of ?30 and rms deviations of about 2.2 ? ...
280 3hwk - Crystal structure of< i> Salmonella typhimurium</i> 2-methylcitrate synthase: Insights on domain movement and substrate specificity 2011 S Chittori, HS Savithri, MRN Murthy - Journal of Structural Biology, 2011 - Elsevier ... In contrast, structural comparison of StPrpC with Mycobacterium tuberculosis GltA1 (MtGltA1; PDB: 3HWK; unpublished results) and Pyrococcus furiosus CS (PfGltA; type-I CS with shorter N-terminal) showed significant similarity in the core structure as well as in the flanking C-terminal extension...
281 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
282 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
283 3i0p - Structural and Functional Insights into (S)-Ureidoglycolate Dehydrogenase, a Metabolic Branch Point Enzyme in Nitrogen Utilization 2012 MI Kim, I Shin, S Cho, J Lee, S Rhee - PloS one, 2012 - dx.plos.org ... structure of the apo form of AllD was solved by molecular replacement with a monomer of E. coli AllD (PDB code 1XRH ... horikoshii OT3 malate dehydrogenase (1V9N; Z-score, 41.1; rmsd, 1.6 ?), EMDH annotated as Entamoeba histolytica malate dehydrogenase (3I0P; Z-score ...
284 3i0p - Helix?helix interactions and their impact on protein motifs and assemblies 2010 N Kurochkina - Journal of Theoretical Biology, 2010 - Elsevier ... Protein, Source, PDB designation. Four-?-helix bundle, Myohemerythrin, Thermiste zostericola, 2 mhr. Hemerythrin, Thermiste discrita, 2hmq. ... Aeropyrum pernix, 2d4a. Entamoeba hystolitica,3i0p. Uridine-diphosphate-galactose 4-epimerase, Trypanosoma brucei, 1gy8. ...
285 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
286 3i3r 3nrr Caracterizao estrutural e avaliao da atividade biolgica de uma nova hipotensina identificada no veneno do escorpio Tityus stigmurus 2016 RJA Machado - 2016 - repositorio.ufrn.br ... This study aimed to carry out the structural characterization and biological evaluation of a new hypotensin identified in T. stigmurus scorpion venom. The cluster TSTI0006C, obtained from the venom gland transcriptome, was analyzed and had its primary structure reduced after ...
287 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
288 3i3r - Structure-Based Targeting of Orthologous Pathogen Proteins Accelerates Antiparasitic Drug Discovery 2017 V Jain, A Sharma, G Singh, M Yogavel - ACS Infectious , 2017 - ACS Publications ... Structures for dihydrofolate reductase (DHFR) inhibitors pyrimethamine, methotrexate, and trimetrexate that are active against P. falciparum, T. brucei, and T. cruzi, respectively. (B) DHFR domain architectures and active site residues are similar in many pathogens: Trypanosoma cruzi (PDB: 3HBB), Cryptosporidium hominis (PDB: 1QZF), Trypanosoma brucei (PDB: 3QFX), Babesia bovis (PDB: 3I3R),. ...
289 3i44 - Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the 2019 S Malhotra, AF Alsulami, Y Heiyun, BM Ochoa, H Jubb- PloS one, 2019 - journals.plos.org We modeled the structure the transmembrane domain and the missing regions between the kinase domain and the transmembrane residue range: 191239, using ( PDB IDs: 1H4I, 3I44 , and 1H4J) as We then mapped the mutation data on to the modeled structure (Fig 6A)
290 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
291 3i4e 3oq8, 3e5b, 3p0x, 3eol Mechanistic Insights into the Catalytic Mechanism and Inhibition of Mycobacterium Tuberculosis Isocitrate Lyase 2019 S Ray - 2019 - ubir.buffalo.edu an attractive target for drug development. 1.4.3 Structure of ICL Aspergillus nidulans [ PDB ID: 1DQU],67 M. tuberculosis [ PDB ID: 1F61, 1F8I, 1F8M, 5DQL],68- 69 Escherichia coli [ PDB ID:1IGW]70, Burkholderia pseudomallei [ PDB ID: 3I4E (paper
292 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 ...
293 3i4e 3p0x Biochemical properties and crystal structure of isocitrate lyase from Bacillus cereus ATCC 14579 2020 SH Lee, D Ki, S Kim, IK Kim, KJ Kim- Biochemical and Biophysical, 2020 - Elsevier 2.5. Structure determination of BcICL. The structure of BcICL was determined using the molecular replacement method with the CCP4 version of MOLREP [24]. The structure of Isocitrate lyase from Burkholderia pseudomallei ( PDB code 3I4E ) was used as a search model
294 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 ...
295 3i4e 3p0x, 3oq8, 3eol, 3e5b Potential Inhibitors for Isocitrate Lyase of Mycobacterium tuberculosis and Non-M. tuberculosis: A Summary 2015 YV Lee, HA Wahab, YS Choong - BioMed Research International, 2015 - hindawi.com ... 1F8M [5]], Escherichia coli [PDB id: 1IGW [6]], Burkholderia pseudomallei [PDB id: 3I4E (paperunpublished ... crystal structure using Ligand Fit module of Discovery Studio 2.1 software (PDB id1F8M ... View at Scopus; V. Sharma, S. Sharma, KHZ Bentrup et al., “Structure of isocitrate ...
296 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.
297 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
298 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.
299 3ido - Structure function relationship of phosphatases from Vibrio choleraeo395 2016 S Nath - 2016 - ir.inflibnet.ac.in ... 1Z12) [5], mouse RPTPA (PDB: 2P4U) [6], yeast LTP1 (PDB: 1D1P) [7] and protozoan parasiteEntamoeba histolytica EhPtp (PDB: 3IDO) [8] are ... Com- parison of the VcLMWPTP-1 structureand surface properties with similar structures in the PDB illuminates its ...
300 3ido - The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis 2019 SB Pereira, M Santos, JP Leite, C Flores- , 2019 - Wiley Online Library We clarified the roles of both proteins through biochemical and structural analysis, pro viding the first A threedimensional protein structure alignment was performed using representative LMWPTP sequences from the eukaryote E. histolytica ( PDB : 3ido ; UniProt:C4LSE7
301 3ido 3jvi Vibrio cholerae LMWPTP-2 display unique surface charge and grooves around the active site: Indicative of distinctive substrate specificity and scope to design specific 2019 S Chatterjee, S Nath, B Ghosh, U Sen- Biochimica et Biophysica Acta (BBA, 2019 - Elsevier The surface properties of VcLMWTP-1, although have some distinct features, resembles closely to that of E. histolytica LMWPTP ( PDB : 3IDO ) This closure at the P-loop is also evident from the structural alignment with an 'open structure ' of apo-MPtpA ( PDB : 2LUO) [41] to the
302 3ido - Cloning, purification, crystallization and preliminary X-ray analysis of two low-molecular-weight protein tyrosine phosphatases from Vibrio cholerae 2012 S Nath, R Banerjee, S Khamrui, U Sen - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... Biol. 215, 403-410.] ) search for a homologous structure showed that the amino-acid sequence of VcLMWPTP-1 possesses the highest identity (43%) to that of protein tyrosine phosphatase from Entamoeba histolytica (PDB entry 3ido ; Seattle Structural Genomics Center for ...
303 3ido 3jvi Atomic resolution crystal structure of< i> Vc</i> LMWPTP-1 from< i> Vibrio cholerae</i> O395: insights into a novel mode of dimerization in the Low molecular Weight 2014 S Nath, R Banerjee, U Sen - Biochemical and Biophysical Research , 2014 - Elsevier ... Several structures of LMWPTP from eukaryotic organism such as human- HCPTPA (PDB: 5PNT) [4], bovine BPTPA (PDB: 1Z12) [5], mouse RPTPA (PDB: 2P4U) [6], yeast LTP1 (PDB: 1D1P) [7] and protozoan parasite Entameoba histolytica EhPtp (PDB: 3IDO) [8] are ...
304 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
305 3ief 3knu Landscape of Intertwined Associations in Multi-Domain Homo-Oligomeric Proteins 2015 SS MacKinnon, SJ Wodak - Journal of molecular biology, 2015 - Elsevier ... In addition, we identified protein structures in the PDB related to each member of our ... We examineddomain re-orientations in these relatives and how the quaternary structure is affected ... This allowedus to characterize the level of structural plasticity in protein families comprising ...
306 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...
307 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
308 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. ...
309 3ijp - Plant DHDPR forms a dimer with unique secondary structure features that preclude higher order assembly 2017 SAJ Watkin, JR Keown, E Richards- Biochemical, 2017 - biochemj.org Cirilli, M., Zheng, RJ, Scapin, G., and Blanchard, JS (2003) The three-dimensional structures of the Structural and mutagenic analysis of relaxed nucleotide specificity Scapin, G., Reddy, SG, Zheng, R., and Blanchard, JS (1997) Three-dimensional structure 490 of Escherichia
310 3ijp 4f3y, 4ywj 4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae structure and interactions with coenzymes and substrate analog 2018 S Pote, SE Pye, TE Sheahan- Biochemical and, 2018 - Elsevier In case of NgDapB, the position of the coenzyme is modeled using structure of PaDapB ( PDB ID from Bartonella henselae, Burkholderia thailandensis, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Thermotoga maritima ( PDB IDs: 3IJP , 4F3Y, 1ARZ, 4YWJ, 3QY9, 1VM6).
311 3ijp - Structure and nucleotide specificity of< i> Staphylococcus aureus</i> dihydrodipicolinate reductase (DapB) 2011 TS Girish, V Navratna, B Gopal - FEBS letters, 2011 - Elsevier ... from Escherichia coli, Mycobacterium tuberculosis, Thermotoga maritima and Bartonella henselae have been determined ( [10], [11] and [18]; PDB:1VM6 (Joint Centre for Structural Genomics) and PDB:3IJP (Seattle Structural Genomics Center for Infectious Disease). ...
312 3ijp - Cloning overexpression purification and characterization of DAPB gene encoding dihydrodipicolinate reductase of pseudomonas aeruginosa PAO1 2016 V Anand - 2016 - ir.inflibnet.ac.in ... preliminary crystallization reports have been published for Staphylococcus aureus (Dommarajuet al., 2010) and Bartonella henselae (PDB code 3IJP) as well. ... biosynthesis enzyme from P.aeruginosa PAOl is an essential step to finally determine its 3-D structure and can ...
313 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
314 3ijp - Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus 2021 S Pote, S Kachhap, NJ Mank, L Daneshian- et Biophysica Acta (BBA, 2021 - Elsevier This paper focuses on structural and mechanistic studies of DapB The structure for DapB has been determined from various bacterial species including Escherichia coli [14], Bartonella henselae [15 Fig. 2. (A) Tetrameric assembly of DapB from V. vulnificus ( PDB ID: 5TEN)
315 3ijp - MOLECULAR MODELING AND DOCKING STUDIES OF DIHYDRODIPICOLINATE REDUCTASE ENZYME (DHDPR) OF STREPTOCOCCUS SUIS AND … 2014 ON Erick, MN Padmanabhan… - Advances in …, 2014 - search.proquest.com ... The current study hypothesized to model structure for DapB gene encoding dihydrodipicolinatereductase enzyme ... et al., 1997 ; PDB:1VM6 (Joint Centre for Structural Genomics) and PDB:3IJP(Seattle Structural ... Structural and mutagenic analysis of relaxed nucleotide specificity. ...
316 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 ...
317 3ijp 4f3y Cloning, expression, crystallization and preliminary structural studies of dihydrodipicolinate reductase from Acinetobacter baumannii 2013 S Kaushik, A Singh, M Sinha, P Kaur? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... 143, 617-623.] ), Bartonella henselae (BhDHDPR; PDB entry 3ijp ; Seattle Structural Genomics Center for Infectious Disease, unpublished work), Burkholderia thailandensis (BtDHDPR; PDB entry 4f3y ; Seattle Structural Genomics Center for Infectious Disease, unpublished ...
318 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 ...
319 3ijp - Molecular cloning, biochemical and biophysical studies of Dihydrodipicolinate reductase of Pseudomonas aeruginosa PAO1 2011 V Anand, A Gautam, D Sareen, TP Singh? - Int. J. Integ. Biol, 2011 - ijib.classicrus.com ... Thermotoga maritima (Pearce et al., 2008) have been characterized both mechanistically and structurally while some preliminary crystallization reports have been published for Staphylococcus aureus (Dommaraju et al., 2010) and Bartonella henselae (PDB code 3IJP) as well. ...
320 3ily - Virtual Screening Studies for Discovery of Novel Inhibitors of Inflammatory Process Targets 2018 MT Scotti, MF Alves- Current, 2018 - ingentaconnect.com The structure -based pharmacophore models were produced with several inhibitor complexes (3PDC, 31 3ANS, 27 3ANT, 3OTQ, 3KOO, 3ILY , 3I28, 1ZD5 and 1VJ540) from the PDB databank (https://www.rcsb.org/ pdb /) [139-144]
321 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);...
322 3iml 3dms, 3hja, 3gtd, 3mbf, 3sth, 3s82, 3qbp, 3l0d, 3kx6, 4oh7, 4xfj, 4tu1 Investigation of intrinsic dynamics of enzymes involved in metabolic pathways using coarse-grained normal mode analysis 2017 SM Meeuwsen, AN Hodac, LM Adams - Cogent , 2017 - Taylor & Francis ... (3IML), and M. avium (3S82) MATs together. The dynamics of 3IML are more similar to the ... 6) toassist in the open and closed conformations of the enzyme. Ornithine transcarbamylase (PDBcode: 4OH7; chains A and B of the homotrimer were ... Visualization of the structure ...
323 3iml 3n58 Identification and Characterization of the Chlamydia trachomatis L2 S-Adenosylmethionine Transporter 2011 R Binet, RE Fernandez, DJ Fisher, AT Maurelli - mBio, 2011 - Am Soc Microbiol ... The alignment was generated using the Tcoffee expresso Web server using Arabidopsis thaliana MAT1 sequence (P23686) and the tertiary sequence of rat MAT1 (PDB ID 1O9T), E. coli MAT (PDB ID 1XRC) and Burkholderia pseudomallei MAT (PDB ID 3IML). ...
324 3iml - Structure of a thermostable methionine adenosyltransferase from Thermus thermophilus HB27 reveals a novel fold of the flexible loop 2016 Y Liu, W Wang, W Zhang, Y Dong, F Han, M Raza - RSC Advances, 2016 - pubs.rsc.org ... sapiens (HsMAT, PDB code: 2P02), Burkholderia pseudomallei (BpMAT, PDB code: 3IML),Thermococcus kodakarensis ... 20 The structure of EcMAT (PDB code: 1RG9, chain A) was selectedas the ... the underlying reason for its thermostability, we solved the crystal structure of apo ...
325 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 ...
326 3iml - Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits 2013 N SHAFQAT, JRC MUNIZ, ES PILKA? - Biochem. J, 2013 - 31.24.0.66 ... sequences include hMAT1A (PDB code 2OBV; Uniprot ID Q00266), hMAT2A (PDB code 2P02; Uniprot ID P31153), rMAT1A (PDB code 1O9T; Uniprot ID P13444), eMAT (PDB code 1RG; Uniprot ID P0A817) and Burkholderia pseudomallei MAT (PDB code 3IML; Uniprot ID ...
327 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. ...
328 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. ...
329 3inn 4ed4 Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity 2014 T Krotzky, T Rickmeyer, T Fober… - Journal of chemical …, 2014 - ACS Publications ... To set up a more challenging task with respect to conformational and structural diversity, we ... serverPISCES of the Dunbrack lab(35) was employed, which kept only PDB structures that agreed ... thesequence identity does not exceed 25%, the method of structure determination is ...
330 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
331 3ixc - Crystal structure and active site engineering of a halophilic -carbonic anhydrase 2020 M Vogler, R Karan, D Renn, A Vancea- Frontiers in, 2020 - frontiersin.org (C) The surface potential of CA_D compared to mesophilic -CA homologs (Escherichia coli, 3tio; Salmonella enterica, 3r3r; Anaplasma phagocytophilum, 3ixc ; Bacillus cereus, 1xhd (A) CA_D (crystal structure ), (B) Cam (crystal structure ) from M. thermophila ( PDB ID: 1qrg
332 3ixc - PIM: Phase Integrated Method for Normal Mode Analysis of Biomolecules in a Crystalline Environment 2013 M Lu, J Ma - Journal of molecular biology, 2013 - Elsevier ... There are totally 29 out of the 65 space groups in this case, shown in the leftmost column of Table 1. In the Protein Data Bank (PDB), 73.3% of the structures belong to this case. ... In the PDB, 24.0% of the structures belong to the case. ...
333 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
334 3ixc - Molecular structure of thermostable and zinc-ion-binding -class carbonic anhydrases 2019 W Wang, Y Zhang, L Wang, Q Jing, X Wang, X Xi- BioMetals, 2019 - Springer are displayed as cartoon diagrams with different colors and are labelled with their respective PDB codes using -TtCA 169 , the 1011 loop is almost the same as 1V67, 1XHD, 2FKO, 3IXC , 4MFG, and However, in the structure of -TtCA 169 , half of the C-terminal -helix is
335 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 ...
336 3ixc - Molecular Docking Studies of Wolbachia Endosymbiont of Brugia Malayi's Carbonic Anhydrase Using Coumarin-chromene Derivatives Towards Designing Anti-filarial 2016 P Malathy, G Jagadeesan, K Gunasekaran - , 2016 - earticle.net ... The BLAST results shows a hexapeptide transferase family protein from Anaplasmaphagocytophilum (PDB ID: 3IXC) having 77% similarity and 54% identity with wBm carbonicanhydrase. Hence the above enzyme is chosen as the template and the 3D structure of carbonic ...
337 3js4 - Superoxide dismutases and superoxide reductases 2014 Y Sheng, IA Abreu, DE Cabelli, MJ Maroney… - Chemical …, 2014 - ACS Publications ... Figure 2. Stereo ribbon diagrams of SODs and SORs: (A) CuZnSOD (PDB code: 1PU0); (B) NiSOD (PDB code: 1T6U); (C) MnSOD (PDB code: 3LSU); (D) FeSOD (PDB code: 3JS4) ...
338 3js4 - Highly Active Yeast MnSOD has a Novel Mechanism Involving Six-coordinate Mn (3+) Species 2012 Y Sheng - 2012 - escholarship.org ... The enzyme structures of four classes of SOD. (A) Homo sapien CuZnSOD (pdb code: 1PU0); (B) Streptomyces coelicolor NiSOD (pdb code: 1T6U); (C) Saccharomyces cerevisiae MnSOD (pdb code: 3LSU); (D) Anaplasma phagocytophilum FeSOD (pdb code: 3JS4). Page 22. ...
339 3jst - Role of tetrachloro-1, 4-benzoquinone reductase in phenylalanine hydroxylation system and pentachlorophenol degradation in Bacillus cereus AOA-CPS1 2020 OA Aregbesola, A Kumar, MP Mokoena- International Journal of, 2020 - Elsevier Three-dimensional structure and homology modelling of the protein were predicted by submitting the amino acid sequence at the SWISS-MODEL tool at The modelled PDB files were submitted to an online tool (PDBsum) for determining the structural summary [34]. 2.12 ... and sequence identity of 59%, followed by PCD/DCoH (PDB: 3JST) from Brucella melitensis,
340 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 ...
341 3jst - Structure and identification of a pterin dehydratase-like protein as a RuBisCO assembly factor in the alpha-carboxysome 2014 NM Wheatley, CD Sundberg, SD Gidaniyan? - Journal of Biological Chemistry 2014 - ASBMB ... diagram. Coordinates and structure factors have been deposited with the PDB ID code 4LOW. ... carboxysome). Data deposition - Atomic coordinates and diffraction data for acRAF have been deposited in the PDB with ID 4LOW. ...
342 3jst 4e98 Elucidation of genes of unknown function in alpha carboxysome operons: acRAF, BMVs and carbon regulatory PII proteins. 2014 NM Wheatley - 2014 - escholarship.org ... B) Structural alignment of acRAF to PCD from Toxoplasma gondii (PDB 2V6T). T. gondii PCD is colored green. C) Structural alignments of active sites among five PCDs shown in green (PDB IDs: 1DC0, 2EBB, 2V6T, 3JST, 4C45). acRAF is shown in magenta. ...
343 3jvh 3u04, 3ke1, 3k14, 3ikf Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function 2014 P Chaskar, V Zoete, UF Röhrig - Journal of chemical information …, 2014 - ACS Publications ... Quality of the structure: resolution <2.5 Å, DPI <0.5 Å, ligand without missing atoms and ... of theligands, we extracted the respective coordinates from the Protein Databank (PDB) file, added ...Protonation states were determined based on pK a values and structural data for some ...
344 3jvi - In Silico Laboratory: Tools for Similarity-Based Drug Discovery 2020 S Lenik, J Konc- Targeting Enzymes for Pharmaceutical Development, 2020 - Springer The output file 1phrA_3jviA.0.rota. pdb contains 3jvi's coordinates superimposed onto 1phr according to Information window contains the name, PDB , and UniProt number of the clicked amino acid Sequence variants that could not be mapped to the protein structure are listed
345 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). ...
346 3k2c - The Schistosoma mansoni cyclophilin A epitope 107-121 induces a protective immune response against schistosomiasis 2019 TT de Melo, MM Mendes, CC Alves, GB Carvalho- Molecular, 2019 - Elsevier The resulting structure was predicted using six templates (4I9Y: e3 sumo-protein ligase Cyclophilin from Homo sapiens, variant A; 1IHG: bovine cyclophilin 40, 3K2C : peptidyl-prolyl cuniculi; 1XO7: Cyclophilin from Trypanosoma cruzithe bovine Cyclophilin 40 ( PDB code: c1ihgA
347 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
348 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).
349 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). ...
350 3k2h - Structural insights into the molecular basis of the ligand promiscuity 2012 N Sturm, J D?saphy, RJ Quinn, D Rognan? - Journal of Chemical Information and Modeling, 2012 - ACS Publications ... To this purpose, we exploited the information in the Protein Data Bank (PDB)19 to identify ligands involved in complexes with different proteins. ... MATERIALS AND METHODS Identification in the sc-PDB of promiscuous ligands and their targets ...
351 3k2h - Characterization of natural product biological imprints for computer-aided drug design applications 2015 N Sturm - 2015 - theses.fr ... Changes in sequence and structure also explain the poor similarity between SB4 inhibitor-binding sites in Mitogen-activated protein (MAP) kinase 14 and MAP kinase 1 (PDB codes: 1bl7, 3erk), and between the antifolate LYA-binding site in human and protozoan thymidylate synthases (PDB codes: 1juj, 3k2h). ...
352 3k2h - Large-scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real 2014 T Krotzky, C Grunwald, U Egerland… - Journal of chemical …, 2014 - ACS Publications ... Again, we searched the PDB for proteins that bind pemetrexed and found six structures: four thymidylate synthases (1JUJ, 1JU6, 3K2H, 4FQS), a folate receptor (4KN2), and a pteridine reductase (2X9G). By culling this set of proteins using PISCES ...
353 3k2h - Global optimization-based inference of chemogenomic features from drug–target interactions 2015 S Zu, T Chen, S Li - Bioinformatics, 2015 - Oxford Univ Press ... In recent years, several non-structure-based methods, which are not limited by the structureinformation have been developed, along the ... Examples of the substructure-domain interactionsvalidated from the PDB database: (A) PDB entry 1u70, (B) PDB entry 3k2h, (C) PDB ...
354 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..
355 3k31 - Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism 2015 SP Kumar, VR Parmar, YT Jasrai… - Journal of Chemical …, 2015 - Springer ... 3 Enoyl-(acyl-carrier protein) reductase Anaplasma phagocytophilum (strain HZ) 3K31 0.25 0.39 ...similarity methods prioritized probable protein targets available from spinach PDB proteome. ...ligand similarity with caffeine, availability of yeast experi- mental structure complex with ...
356 3k5p - 3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis 2019 N Paczia, J Becker-Kettern, JF Conrotte- Biochemistry, 2019 - ACS Publications Structural Biology Unit, CIC bioGUNE Technological Park of Bizkaia, 48160 Derio , Vizcaya , Spain. IKERBASQUE, Basque Foundation for Here, we provide a detailed biochemical and sequence structure relationship characterization of the yeast PHGDH homologues
357 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 ...
358 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)...
359 3k9w - Kinetic, Thermodynamic, and Structural Insight into the Mechanism of Phosphopantetheine Adenylyltransferase from< i> Mycobacterium tuberculosis</i> 2010 TJ Wubben, AD Mesecar - Journal of molecular biology, 2010 - Elsevier ... 21 Enteroccoccus faecalis, 22 and Helicobacter pylori; 23 and Staphylococcus aureus in complex with 3'-phosphoadenosine 5'-phosphosulfate, 24 Burkholderia pseudomallei in complex with hydrolyzed dPCoA [Protein Data Bank (PDB) ID 3K9W; unpublished], and ...
360 3k9w 3pxu Characterization of Phosphopantetheine Adenylyltransferase: A Potential, Novel, Antibacterial Target 2013 T Wubben - 2013 - indigo.lib.uic.edu ... PDB Protein Data Bank PEG polyethylene glycol PhP 4'-phosphopantetheine Pi orthophosphate ...root mean standard deviation rpm revolutions per minute SAR structure-activity relationship ...thermodynamic, and structural characterization of M.tuberculosis and B.anthracis PPAT ...
361 3k9w - Structural and functional characterization of type three secretion associated proteins from Yersinia enterocolitica and vitamin biosynthesis pathway proteins from 2016 R Chatterjee - 2016 - ir.inflibnet.ac.in Crystal structures of homologues of SycB from PDB (SycD[2VGX], IpgC[3- GYZ], PcrH[2XCC]) showed that Consensus server of secondary structure prediction showed that SycB has 75.7% of helix and rest of Expression, Purification, Structural and Functional Analysis of SycB
362 3k9w - Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa 2016 R Chatterjee, A Mondal, A Basu, S Datta - Biochimica et Biophysica Acta ( , 2016 - Elsevier ... 5-phosphosulfate [PDB ID: 3OTW, 3NV7] [29] and Burkholderia pseudomallei in complex withhydrolyzed dPCoA [PDB ID: 3K9W] [30]. ... was solved using PHASER [38] and by utilizing E. coliphosphopantetheine adenylyltransferase (1HIT chain A) as a starting structure. ...
363 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
364 3k9w - Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation 2011 T Wubben, AD Mesecar - Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2011 - scripts.iucr.org ... To date, a number of X-ray crystal structures of PPAT orthologs have been determined [PDB entries 1b6t (Izard & Geerlof, 1999 [Izard, T ... 404, 202-219.] ), 3k9w (Edwards et al., 2011 [Edwards, TE, Leibly, DJ, Bhandari, J., Statnekov, JB, Phan, I., Dieterich, SH, Abendroth, J., Staker ...
365 3kc6 - Inhibition of Avian Influenza A Virus Replication in Human Cells by Host Restriction Factor TUFM Is Correlated with Autophagy 2017 SM Kuo, CJ Chen, SC Chang, TJ Liu, YH Chen - mBio, 2017 - Am Soc Microbiol ... (B) Modeling of the A/Anhui/1/2013(H7N9) virus PB2 CTD based on the A/Vietnam/1203/2004( H5N1) virus ( PDB ID 3KC6 ). ... as GTP-binding D1), and thus, the lack of association between chTUFM and PB2 627 E may be due to these in sequence and structure differences in ...
366 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
367 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. ...
368 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. ...
369 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 ...
370 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 ...
371 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). ...
372 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....
373 3khp - Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of Rv0241c (HtdX) from Mycobacterium tuberculosis H37Rv 2013 R Biswas, D Dutta, AK Das - Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... PDB entry, Identity (%), Query cover (%), Reference. 1pn2, 47, 10, Koski et al. (2004 [Koski, MK, Haapalainen, AM, Hiltunen, JK & Glumoff, T. (2004). ... F66, 272-274.] ). 3khp, 36, 19, Seattle Structural Genomics Center for Infectious Disease (unpublished work). 3oml, 33, 37, Haataja ...
374 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
375 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 ...
376 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 ...
377 3kjr - Are homology models sufficiently good for free-energy simulations? 2012 S Genheden - Journal of chemical information and modeling, 2012 - ACS Publications ... factor IXa (pdb code: 1rfn(36)) with 44% sequence identity and protein C (pdb code: 1aut ... Suitable template proteins for dhfr were found by a FASTA search(38) of the protein databank. ... The results of the FASTA search are summarized in Table 1. Finally, 2bl9, 3kjr, and 2oip were ...
378 3knu - Dynamics of substrate interactions in tRNA (m1G37) methyltransferase: Implications for drug discovery 2012 MK Palesis - 2012 - scholarscompass.vcu.edu ... The secondary structure of specific sequences is illustrated above the alignment. ... Page 29. 9 Figure6. Structural alignment of TrmD from different bacterial species: Anaplasma phagocytophilum(royal blue, PDB ID: 3KNU), Bartonella henselae (cyan, PDB ID: 31EF ...
379 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
380 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)).. ...
381 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 ...
382 3kre - NOVEL APPLICATIONS OF SPERMINE AND DERIVATIVES THEREOF 2019 W Pan, W Zhu- US Patent App. 16/334,273, 2019 - freepatentsonline.com Thermotoga maritime (1KUT), Clostridium perfringens (3NUA), Ehrlichia chaffeensis ( 3KRE ), Geobacillus kaustophilus On the basis of the above results, the crystal structure conformations in of Saccharormyces cerevisiae ( PDB : 2CNQ) and Escherichia coli ( PDB : 2GQS) are
383 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 ...
384 3kre - Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of SAICAR synthase from Streptococcus suis serotype 2 2010 X Cheng, G Lu, J Qi, H Cheng, F Gao? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2010 - scripts.iucr.org ... F62, 335-339.] ), Ehrlichia chaffeensis (PDB code 3kre ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Pyrococcus horikoshii OT3 (Manjunath et al., 2010 [Manjunath, K., Jeyakanthan, J., Nakagawa, N., Shinkai, A., Yoshimura, M., Kuramitsu, S ...
385 3kre - COMPOUNDS WEAKENING SAICAR SYNTHETASE ACTIVITY AND APPLICATIONS 2019 W Pan, W Zhu- US Patent App. 16/334,256, 2019 - freepatentsonline.com 3R9R), Thermotoga maritime (1KUT), Clostridium perfringens (3NUA), Ehrlichiachaffeensis ( 3KRE ), Geobacilluskaustophilus (2YWV basis of the above results, the crystal structure conformations in Saccharormyces cerevisiae ( PDB : 2CNQ) and Escherichia coli ( PDB : 2GQS)
386 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),
387 3krs - Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations 2011 S Yun, HR Guy - Journal of Molecular Graphics and Modelling, 2011 - Elsevier ... patterns and high resolution (less than 2.0 ? resolution) were selected for this study: a human serum retinol-binding protein (RBP with PDB ID 1JYD) [24], a regulator of G-protein signaling (RGS4 with PDB ID 1EZT) [25], and triosephosphate isomerase (TIM with PDB ID 3KRS). ...
388 3krs - Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins 2012 PG Vasudev, M Banerjee? - Proteins: Structure, Function, and Bioinformatics, 2012 - Wiley Online Library ... acts as the hydrogen bond acceptor. In the available data set of 24 TIM crystal structures, there are three examples with Asn at 119, all of which (PDB IDs:1O5X, 3KRS, 1AW1) exhibit similar motifs. Interestingly, three examples with Gln at position 119 illustrated in ...
389 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 )
390 3kw3 - Identification of a new alanine racemase in Salmonella Enteritidis and its contribution to pathogenesis 2018 S Ray, S Das, PK Panda- Gut pathogens, 2018 - gutpathogens.biomedcentral.com From I-Tasser and BLAST analyses, SEN4016 (359 amino acid residues) showed significant structural identity of 91% with Chain A, Y274f Alanine Racemase from E. Coli (PDB-ID-4WR3) with an estimated score of 0.97 ± 0.05 and C-score of 1.82. Similarly, SEN3897 having a score of 0.85 ± 0.08 and C score of 1.00 showed 42% identity with Chain A, Alanine Racemase from Bartonella henselae (PDB-ID-3KW3) and SEN1235 with a C score of 1.79 and estimated score of 0.97 ± 0.05 showed 48% identity with chain A of alanine r
391 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). ...
392 3kw3 - Computational approach on drug targeted proteins in streptococcus pneumoniae Molecular modelling inhibitor design and docking studies 2016 TM Reddy - 2016 - ir.inflibnet.ac.in ... Sequence alignment of Sp-AIr model with crystal structure alanine racemase (1SFT) based onsequence ... Air, indicates it closely related with 1SFT compare with other PDB's (2SFP, ... 2DY3 Air,1 SFT 2SFP 1EPV 1XQK 3HA1 2VD9 2VD8 3HUR ----- 3COS 3KW3 1RCQ 20D0 I ...
393 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%). ...
394 3kx6 - Structural and Functional Divergence of the Aldolase Fold in Toxoplasma gondii 2014 ML Tonkin, AS Halavaty, R Ramaswamy, J Ruan… - Journal of molecular …, 2014 - Elsevier ... We also determined the structure of TgDPA in a different crystal form (data not shown but structuredeposited with identifier PDB ID 3QYQ ... However, preliminary sequence and structural comparisonof several dR5P aldolases (rmsd of < 2.0 Å and sequence homology as low ...
395 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 ...
396 3kzx - Sequence specificity between interacting and non-interacting homologs identifies interface residuesa homodimer and monomer use case 2015 Q Hou, BE Dutilh, MA Huynen, J Heringa - BMC , 2015 - biomedcentral.com ... all 11 monomeric C1-type HAD Hydrolase group (2NYV, 2HSZ, 2HI0, 2AH5, 4EX6, 3MC1, 3D6J,3KBB, 3KZX, 2HDO, 3SD7). ... 6 shows the interface and predicted interface sites in the structure. ...a Secondary stucture of two chains of PDB 3QGM (chain C and D). The interface is in ...
397 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. ...
398 3kzx - Multi-Scale Investigation of Protein-Protein Interactions 2017 Q Hou - 2017 - dare.ubvu.vu.nl ... The protein structure on the back cover is PDB 3E8L. ... Sequence level Although an increasing number of protein structures have become available, there is still a lack of structural data for most protein sequences, which is called the 'sequence- structure gap' [Rost and Sander ...
399 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
400 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). ...
401 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
402 3l56 - Molecular mechanisms of transcription and replication of the influenza A virus genome 2011 S Zhang, T Toyoda - Frontiers in Biology, 2011 - Springer ... (b) The electrostatic potential of PB2 3/3 E627 was calculated using the GRASP program. Modified from Fig. 2 of Kuzuhara et al. (2009b). G: PB2 C-terminal NLS. PDB accession number:3L56. Figures were rendered in PyMOL (http://www.pymol.org/). ...
403 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). ...
404 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). ...
405 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), ...
406 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. ...
407 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 ...
408 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 ...
409 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. ...
410 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
411 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 ...
412 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. ...
413 3laa - Analysis of the BadA stalk from Bartonella henselae reveals domain‐specific and domain‐overlapping functions in the host cell infection process 2012 PO Kaiser, D Linke, H Schwarz, JC Leo… - Cellular …, 2012 - Wiley Online Library ... The structures are the YadA head (PDB ID: 1PH9) of Y. enterocolitica (Nummelin et al., 2004),the BpaA head ... structural motifs matches the colouring of the schematic diagram in A. The depictedstructural motifs of 3LAA occur in the inverse order in the original structure to that ...
414 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
415 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. ...
416 3laa 3s6l, 4lgo Non-adaptive evolution of trimeric autotransporters in Brucellaceae 2020 MR Rahbar, M Zarei, A Jahangiri, S Khalili- Frontiers in, 2020 - ncbi.nlm.nih.gov domain from Haemophilus influenzae genome ( PDB ID:1S7M; Yeo et al., 2004); structure of the parallel beta-roll collagen-binding domain of Yersinia enterocolitica adhesin YadA ( PDB ID: 1P9H Batch analyzes of the dataset suggested the existence of a few structural domains
417 3laa - Functional Analysis of the Polymorphic Membrane Protein Family of Chlamydia 2013 V Grinblat-Huse - 2013 - archive.hshsl.umaryland.edu ... The trimeric autotransporter adhesin head domain [RCSB indentifier 3LAA] from Burkholderia pseudomallei and the outer membrane adhesin/invasin [RCSB identifier 1K24] from Neisseria meningitidis were also used to attempt a structure prediction ...
418 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
419 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. ...
420 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 ...
421 3ld9 3v9p Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of thymidylate kinase (TTHA1607) from Thermus thermophilus HB8 2013 SK Chaudhary, J Jeyakanthan? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... aureus (PDB entry 4f4i ; Midwest Center for Structural Genomics, unpublished work), Burkholderia thailandensis (PDB entry 3v9p ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Ehrlichia chaffeensis (PDB entry 3ld9 ; Leibly et al., 2011 [Leibly ...
422 3lg6 - Identification and clarification of the role of key active site residues in bacterial glutathione< i> S</i>-transferase zeta/maleylpyruvate isomerase 2011 T Fang, DF Li, NY Zhou - Biochemical and Biophysical Research Communications, 2011 - Elsevier ... 2. Phylogenetic relationships of NagL (PDB ID, 2JL4) and other representative cGSTs from the protein data bank. ... delta (1V2A, 1R5A, 3F6F, 3EIN, 1PN9, 1JLV, 3F63 and lJLW), omega (1EEM), tau (2VO4, 1OYJ and 1GWC) and zeta (1FW1, 1E6B, 2JL4, 3NIV, 3LG6 and 2CZ2). ...
423 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. ...
424 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
425 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 ...
426 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)
427 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 ...
428 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. ...
429 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
430 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
431 3m1x - Protein structure prediction guided by crosslinking restraints–A systematic evaluation of the impact of the crosslinking spacer length 2015 T Hofmann, AW Fischer, J Meiler, S Kalkhof - Methods, 2015 - Elsevier ... Based on the structure of calmodulin (PDB entry 2ksz) the average Cβ–Nz, Cβ–Cγ, Cβ–Cδ,Cβ–N H2 , and Cβ–S G distances ... Structure, Uniprot, Resolution [Å], Molecular weight [Da],Sequence length [aa], Lys portion [%], α-helix [%], β-sheet ... 3m1x, C4LXT9, 1.2, 15882, 138, 7, ...
432 3m4s - Ultratight crystal packing of a 10 kDa protein 2013 S Trillo-Muyo, A Jasilionis, MJ Domagalski? - Acta Crystallographica Section D Biological Crystallography, 2013 - scripts.iucr.org ... 2xge ). Cases for which the solvent content was artificially low owing to long missing N- and C-terminal fragments were not considered either (PDB entries 2xnq , 2duy , 2axo , 3bqh , 2f9l , 3m4s , 3nzl , 2xjx , 4eti , 2ds8 and 1vfq ). ...
433 3m4s - Crystal structures of RidA, an important enzyme for the prevention of toxic side products 2016 X Liu, J Zeng, X Chen, W Xie- Scientific reports, 2016 - nature.com 2DYY, dirty violet), and Entamoeba histolytica l-PSP ( PDB code 3M4S , gray) respectively unpublished), and a putative endoribonuclease l-PSP from Entamoeba histolytica ( PDB code3M4S, unpublished AtRidA is highly similar to other RidA family members in structure , and their
434 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. ...
435 3mc4 - Crystal structure of serine acetyl transferase from< i> Brucella abortus</i> and its complex with coenzyme A 2014 S Kumar, N Kumar, N Alam, S Gourinath - Biochimica et Biophysica Acta ( , 2014 - Elsevier ... max SAT [10] have been previously published. The coordinates of a crystal structure of SAT from Brucella melitensis has also been deposited at the Protein Data Bank (PDB code: 3MC4). SATs from E. coli, B. melitensis, H. influenzae ...
436 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 ...
437 3md7 - Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway 2011 SM He, M Wathier, K Podzelinska, M Wong? - Biochemistry, 2011 - ACS Publications ... distances in angstroms. (d) Wall-eyed stereoview of the PhnP?orthovanadate complex superimposed with B. melitensis phosphodiesterase (PDB entry 3md7) bound to guanosine 5'-monophosphate (gray sticks). PhnP residues ...
438 3md7 3urr, 3uw3, 3swo, 3mqd The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment 2013 S Chakraborty, R Venkatramani, BJ Rao… - …, 2013 - ncbi.nlm.nih.gov ... PDB, NRes, NStructures, Specificity. ... based on the 'sequence to structure to function' paradigmis contingent upon the availability of its 3D-structure. The rapidly developing field of nextgeneration sequencing has exacerbated the bottleneck of obtaining structural data using ...
439 3md7 - Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cAMP and cGMP 2014 Y Tian, W Cui, M Huang, H Robinson, Y Wan - Biochemistry, 2014 - ACS Publications ... structure. The atomic model was built with O(39) and refined with REFMAC.(40). The yPDE1 structure was compared with structures in the Protein Data Bank by the online program Dali (http://www.ebi.ac.uk/Tools/structure/dalilite). ...
440 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. . ...
441 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
442 3men - Design of Drugs by Filtering Through ADMET, Physicochemical and Ligand-Target Flexibility Properties 2018 M Martnez-Archundia, M Bello, J Correa-Basurto- Rational Drug Design, 2018 - Springer the three-dimensional model of the human HDAC6, considering some of the crystal structures available for this protein, which maintained some structural identities (2VCG (37%), 1ZZ0 (37%), 1C3P (29%), 3MEN (36%), 3COY 4. Finally, the crystal structure of PDB : 3F07 was
443 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 ...
444 3men - Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases 2011 PM Lombardi, HD Angell, DA Whittington, EF Flynn? - Biochemistry, 2011 - ACS Publications The recently solved X-ray crystal structure of the Burkholderia pseudomallei APAH dimer (PDB ID: 3MEN; 34% sequence identity with M. ramosa APAH) contains a 16-residue L2 loop insertion (A79−R101) between helices B2 and B3.
445 3men - Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery 2019 V Chahal, S Nirwan, R Kakkar- Physical Sciences Reviews, 2019 - degruyter.com Figure 2: Steps involved in homology modeling for 3D structure prediction sequences of proteins with known 3D structures available in various depositories such as PDB , using the In some cases, a single template is not enough to provide the complete structural information ... This catalytic domain was modeled using the I-TASSER server [98] by exploiting the solved crystal structures of some HDAC proteins having structural identities (2VCG (37%), 1ZZ0 (37%), 1C3P (29%), 3MEN (36%), 3COY (47%),
446 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 ...
447 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
448 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), ...
449 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 ...
450 3meq - Asymmetric reduction of diketones by two Gluconobacter oxydans oxidoreductases 2012 P Schweiger, H Gross, J Zeiser? - Applied Microbiology and Biotechnology, 2012 - Springer ... identity, >70 % similarity) to other alcohol dehydrogenase with known 3-D structure, for example, to zinc-dependent alcohol dehydrogenases from Brucella suis (PDB, 3MEQ_A), Pseudomonas ... 2004), 3MEQ from B. suis, and 1RJW from G. stearthermophilus (Ceccarelli et al. ...
451 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 ...
452 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
453 3meq - Adaptations to high salt in a halophilic protist: differential expression and gene acquisitions through duplications and gene transfers 2017 T Harding, AJ Roger, AGB Simpson- Frontiers in microbiology, 2017 - frontiersin.org WP_041596283.1), and sequences for characterized NADPH-dependent enzymes from S. cerevisiae (1Q1N), P. perezi (1P0C), Helicobacter pylori (3TWO), Populus tremuloides (1YQD) and Catharanthus roseus (5H81), and for NADH-dependent enzymes from Moraxella sp. (4Z6K), Geobacillus stearothermophilus (3PII), Ralstonia eutropha (3S1L), Brucella suis (3MEQ), and Pseudomonas aeruginosa (1LLU). (B) Maximum-likelihood phylogenetic tree for zinc-dependent alcohol dehydrogenase showing strongly supported clustering (gray
454 3meq - ENZYMATIC REDUCTION BY ALCOHOL DEHYDROGENASE TA1316 FROM Thermoplasma acidophilum 2017 M Guzmn-Rondrguez, L Santos - Revista Mexicana de Ingeniera , 2017 - redalyc.org ... 3MEQ Brucella melitensis ADH Tetramer Zn +2 , Cl, Na + 0.930 To be published 1R37 Sulfolobussolfataricus ADH Tetramer Zn +2 0.929 (Esposito et al. 2003) ... Structural analyses displayed by thePDB platform showed the crystal structure of Pyrobaculum aerophilum ...
455 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
456 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 ...
457 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. ...
458 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 ...
459 3mmt - The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis 2020 M Sharma, P Abayakoon, Y Jin, R Epa, JP Lingford - 2020 - chemrxiv.org Figure S15. Closed conformations of PfkB, TPK and SF kinases indicate close structural rela- tionship EcYihVADPMgSF structure reveals KRN sulfonate recognition triad in YihV A, FBPA from Bartonella henselae forms homotetramers ( 3MMT . pdb ),{, 2011 #8494} FBPA from
460 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. ...
461 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- ...
462 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
463 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
464 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
465 3mx6 - Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity 2019 SC Bala, N Haque, V Pillalamarri, R Reddi- International journal of, 2019 - Elsevier 3MX6 , R. prowazekii, 99% (C), 1% (L) Based on this analysis, MetAP1n has different active site architecture and hence has a substrate preference for leucine in addition 3c. Column 2 describes the result analysis of the HSSP file associated with EcMetAP1a structure ( PDB : 1C21
466 3mx6 - P1 Residue-Oriented Virtual Screening for Potent and Selective Phosphinic (Dehydro) Dipeptide Inhibitors of Metallo-Aminopeptidases 2020 M Talma, A Mucha- Biomolecules, 2020 - mdpi.com 20 to keep the size similar to the grid from the first step (36 for PDB : 2EK8 In general, the structure proposed here surpasses known inhibitors As the overall architecture of the S1 binding sites of porcine, bacterial, and protozoal APNs is rather conserved, the advantageous ... Table 1. Cont. Rickettsia prowazekii 3MX6 [41]
467 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. ...
468 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
469 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 ...
470 3ndn - Bacterial methionine biosynthesis 2014 MP Ferla, WM Patrick - Microbiology, 2014 - Soc General Microbiol ... 2). Its presence in P. aeruginosa and P. putida has been discussed (Foglino et al., 1995; Alaminos & Ramos, 2001), and an unpublished structure of a Mycobacterium tuberculosis O-succinylhomoserine thiolase has been deposited in the Protein Data Bank (PDB ID 3NDN). ...
471 3ndn - Characterization of the Side-Chain Hydroxyl Moieties of Residues Y56, Y111, Y238, Y338, and S339 as Determinants of Specificity in E. coli Cystathionine beta-Lyase 2011 PH Lodha, SM Aitken - Biochemistry, 2011 - ACS Publications ... figure Scheme 2. Observed Contacts of the PLP-AVG External Aldimine Active Site of eCBL a. a The dotted lines represent putative hydrogen bond distances of ?3.3 ? between heteroatoms. The image was constructed using ChemDraw and PDB entry 1CL2.(3). ...
472 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 ...
473 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
474 3nf4 - Mycobacterium tuberculosis Utilizes a Unique Heterotetrameric Structure for Dehydrogenation of the Cholesterol Side Chain 2013 ST Thomas, NS Sampson - Biochemistry, 2013 - ACS Publications ... 16) FAD binding and CoA binding in published ACAD Protein Data Bank (PPDB) structures ... between FAD and several ACADs in reported crystal structures (PDB entry in ... 2WBI) and bacterial ACADS from Megsphaera elsdenii (1BUC) and Mycobacterium thermoresistibile (3NF4 ...
475 3nf4 3pfd Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis 2013 X Duan, L Zhang, D Zhou, K Ji, T Ma? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... different protein structures with the highest protein-sequence similarity to DszC [PDB entries 2vig ... 277, 12200-12207.] ), 3nf4 (24% identity; Seattle Structural Genomics Center for Infectious Disease ... and structure factors have been deposited in the Protein Data Bank (Bernstein et ...
476 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. ...
477 3nf4 - Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity 2017 T Hino, H Hamamoto, H Suzuki, H Yagi - Journal of Biological , 2017 - ASBMB ... replacement search models using MolRep (44). The polyalanine model from Mycobacterium thermoresistibile ( PDB ID: 3NF4 ) showed the highest score. After application of the ... All other structures were solved by molecular replacement of the apo-TdsC structure using ...
478 3nf4 - Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate 2017 T Hino, H Hamamoto, H Suzuki, H Yagi- Journal of Biological, 2017 - Elsevier 2B). This domain architecture and quaternary structure are also seen for the acyl-CoA dehydrogenase superfamily (25), and the structure of TdsC is very similar to that of DszC (2122, 23 Structure of FMN-bound TdsC FMN binding to TdsC resulted in no global structural changes
479 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
480 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) ...
481 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
482 3nfw - Biochemical properties and crystal structure of the flavin reductase FerA from Paracoccus denitrificans 2016 V Sedlek, T Klumpler, J Marek, I Kuera - Microbiological Research, 2016 - Elsevier ...Sequence and structural comparisons of FerA with a flavin reductase like domain protein family (PF01613). 3NFW E5Q9D7 NmoB Mycobacterium thermoresistibile ...
483 3nfw - Crystallization and preliminary X-ray analysis of the reductase component of p-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii 2012 W Oonanant, J Sucharitakul, P Chaiyen? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2012 - scripts.iucr.org ... All of these structures share the same protein fold and lack the extra C-terminal domain found in C 1 . Recently, the structure of NTA monooxygenase component B from Mycobacterium thermoresistibile (PDB entry 3nfw ; Zhang et al., 2011 [Zhang, Y., Edwards, TE, Begley, DW ...
484 3nfw - The C-terminal Domain of 4-Hydroxyphenylacetate 3-Hydroxylase from Acinetobacter baumannii Is an Autoinhibitory Domain 2012 T Phongsak, J Sucharitakul, K Thotsaporn? - Journal of Biological Chemistry, 2012 - ASBMB ... Recently, the structure of the reductase of nitrilotriacetate monooxygenase (NTA_MoB; Protein Data Bank code 3NFW) from Mycobacterium thermoresistibile has been reported (43). However, NTA_MoB (189 residues) is smaller than cB from Chelatobacter sp. (335 residues). ...
485 3ng3 - Structural insight for substrate tolerance to 2-deoxyribose-5-phosphate aldolase from the pathogen Streptococcus suis 2016 TP Cao, JS Kim, MH Woo, JM Choi, Y Jun, KH Lee - Journal of , 2016 - Springer ... avium DERA (MaDERA, PDB code: 3NG3) as a search mo- del (Baugh et al., 2015)using the CCP4i program MOLREP (Vagin and Teplyakov, 2010). The FL-SsDERAstructure was used as a search model for SL-SsDERA. ...
486 3ngf - Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae 2014 M Shahbaaz, F Ahmad, MI Hassan - 3 Biotech, 2014 - Springer ... was used for structure- based function annotation and for predicting structural motifs associated ...by DALI server that compares the target structure with known structure submitted in PDB. Thesecondary structure elements are computed from atomic resolution protein structures of ...
487 3ngj - Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1, 3-butanediol 2020 T Kim, PJ Stogios, AN Khusnutdinova, K Nemr- Journal of Biological, 2020 - ASBMB DERA structures as the best matches, including the Entamoeba histolytica DeoC ( PDB code 3NGJ ; Z score RMSD, 0.6 ; 66% sequence identity), and L. brevis DERA E78K mutant ( PDB code 4XBS; Z Based on the BH1352 structure , its active site is located inside of the -barrel
488 3ngj - Characterization and application of a newly synthesized 2-deoxyribose-5-phosphate aldolase 2013 ZY You, ZQ Liu, YG Zheng, YC Shen - Journal of industrial microbiology & Biotechnology, 2013 - Springer ... The crystal structures of DERAs from Entamoeba histolytica (PDB accession NO. 3NGJ) and Thermotoga maritima (PDB accession NO. 3R12) were used as templates. ... 3NGJ, resolution 1.70 A?) and Thermotoga maritima (54.3 % identity; PDB accession no. ...
489 3njd 3svk Protein 3-D Structure Representation for Alignment-Free Comparison and Structural Motif Discovery of Proteins, and Hierarchical Protein Classification 2015 S Singh - 2015 - search.proquest.com ... a lot more diversity and complexity, rather than having a simple, unique rigid structure, and that ...of a growing number of methods, there is no widely accepted 3-D structural alignment method.None of the current methods for searching PDB are guaranteed to find true matches in ...
490 3nrr - Pharmacoinformatic Study on the Selective Inhibition of the Protozoan Dihydrofolate Reductase Enzymes 2017 VK Sharma, S Abbat, PV Bharatam - Molecular Informatics, 2017 - Wiley Online Library ... The three dimensional crystal structure with PDB IDs, 3INV for AdDHFR (48.82%), HmmDHFR (50.24 ... 50.72 %), LdDHFR (50.49 %), and LmDHFR (50.98%), 4EIL for TtDHFR (37.57%), 3NRR for BgDHFR ... drug design process.[46] It was observed that the 3D structure of the ...
491 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 ...
492 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) ...
493 3nrr 3i3r Homology modeling, vasorelaxant and bradykinin-potentiating activities of a novel hypotensin found in the scorpion venom from Tityus stigmurus 2015 RJA Machado, LGM Junior, NKV Monteiro… - Toxicon, 2015 - Elsevier ... thymidylate synthase from B. bovis with dUMP, Ralitrexed and NADP (PDB ID: 3NRR, ChainA ... Protein Data Bank are listed here in increasing order of identity: X-ray structure dihydrofolatereductase/thymidylate synthase from B. bovis at 2.35 Å resolution (PDB ID: 3I3R ...
494 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
495 3nwo - The crystal structure of the amidohydrolase VinJ shows a unique hydrophobic tunnel for its interaction with polyketide substrates 2014 Y Shinohara, A Miyanaga, F Kudo, T Eguchi - FEBS letters, 2014 - Elsevier ... method using the Molrep program [16], with the crystal structure of the putative proline iminopeptidase Mycobacterium smegmatis (PDB code: 3NWO) being used ... The resulting coordinates and structure factors have been deposited in the Protein Data Bank (PDB code: 3WMR) ...
496 3nwo - The rise and fall of anandamide: processes that control synthesis, degradation, and storage 2021 RG Biringer- Molecular and Cellular Biochemistry, 2021 - Springer This manuscript discusses the key enzymes in AEA homeostasis, in terms of structure , reaction specificity, enzymatic activity, regulation, and tissue and cellular expression patterns with a focus on the human isoforms involved. ... No X-ray structures or posttranslational modifications have been reported. There are two potential structural model templates suggested on the SWISS-MODEL website [14], template 3nwo.1.A and template 5mxp.1.B. hABHD4 is produced
497 3nxs - Strategies for purifying variants of human rhinovirus 14 2C protein 2014 T S?ra, R Konrat, T Skern - Protein expression and purification, 2014 - Elsevier ... Score, Entry name, PDB identifier. 6198, Human nuclear valosin containing protein like (Nvl), C-terminal AAA?ATPase domain, 2X84. ... 2887, Crystal structure of LAO/AO transport system from Mycobacterium smegmatis bound to GDP, 3NXS. ...
498 3o0h - Sulphur (lone pair) interactions with FAD in flavoenzymes 2018 RFN Silva, ACS Sacco, I Caracelli- Zeitschrift fur, 2018 - eprints.sunway.edu.my Finally, in the 22 SOX enzymes found in PDB , there were 45 monomers having FAD S(lp)(FAD) interactions in three examples of GR enzymes: (a) 1K4Q [64], (b) 3O0H [64] and with FAD via S(lp)(FAD) interactions that pro- vide stability to the secondary structure and
499 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
500 3o0h - Sulfur (lone-pair) interactions with FAD in flavoenzymes 2018 RFN Silva, ACS Sacco, I Caracelli- Zeitschrift fr, 2018 - degruyter.com The interactions of π-systems with lone-pairs of electrons are known and have been described in biological systems, involving lone-pairs derived from metals, metalloids, sulphur, oxygen and nitrogen. This study describes a bibliographic survey of the disulphide-bound sulphur(lone-pair) interactions with -systems residing in the flavin ad Also, the S(lp)…π(FAD) interaction in the 1K4Q [64] and 3O0H [65] proteins show the orientation of sulphur-lp to the Ct(U) centroid, F
501 3o0h - Structural analysis of protein-small molecule interactions by a crystallographic and spectroscopic approach 2017 R Fagiewicz - 2017 - core.ac.uk Uniprot and/or PDB database. In green is highlighted best identity of available biocrystallography reached the mature age and transformed into structural biology. doing extensive work in the structure determination by employing more and more advanced technologies
502 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 ...
503 3o0m - Characterization of Mycobacterial Flap Endonuclease FenA and RNA Helicase HelY 2018 MLL Uson - 2018 - search.proquest.com There, she focused on the detection of circulating tumor cells and structural characterization of EphA3, a 122 Figure 4.3 Manganese ions in the FenA active site ..... 126 Figure 4.4 Active site architecture and structure -guided mutagenesis
504 3o0m - The DNA repair repertoire of Mycobacterium smegmatis FenA includes the incision of DNA 5'flaps and the removal of 5'adenylylated products of aborted nick ligation 2017 ML Uson, S Ghosh, S Shuman- Journal of bacteriology, 2017 - Am Soc Microbiol MSMEG_5871 (Rv0759c) has not been characterized. MSMEG_5028 (Rv1262c) has been characterized structurally (PDB entry 3O0M), but its biochemical activity is uncharted.
505 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
506 3o0m - Evolutionary coupling methods in de novo protein structure prediction 2016 S Seemayer - 2016 - edoc.ub.uni-muenchen.de On homomeric proteins, intermolecular couplings (red) have to be disentangled from intramolecular couplings (yellow) for de novo structure prediction to succeed (representative contacts mapped on PDB code 3O0M)
507 3o0m - Structural Insights into the Novel Diadenosine 5′,5‴-P1,P4-Tetraphosphate Phosphorylase from Mycobacterium tuberculosis H37Rv 2011 S Mori, K Shibayama, JI Wachino, Y Arakawa - Journal of Molecular Biology, 2011 - Elsevier ... Homo sapiens fragile HIT protein [Fhit; Protein Data Bank (PDB) IDs: 6FIT and 1FHI; Z-score = 16.1 and 15.8, respectively], which is a HIT family Ap n A hydrolase; [11] and [12] Zn-bound HIT family protein from Mycobacterium smegmatis (MSMEG5028; PDB ID: 3O0M; Z-score ...
508 3o0m - The DNA Repair Repertoire of Mycobacterium smegmatis FenA Includes the Incision of DNA 5 Flaps and the Removal of 5 Adenylylated Products of Aborted Nick 2017 ML Uson, S Ghosh, S Shuman - Journal of bacteriology, 2017 - Am Soc Microbiol ... IMPORTANCE Structure -specific DNA endonucleases are implicated in bacterial DNA replication, repair, and recombination, yet there is scant knowledge ... We discuss the properties of mycobacterial FenA in light of insightful structural studies of eukaryal flap endonucleases (11 ... MSMEG_5028 (Rv1262c) has been characterized structurally (PDB entry 3O0M), but its biochemical activity is uncharted.
509 3o2e - Sinorhizobium meliloti YrbA binds divalent metal cations using two conserved histidines 2020 T Roret, G Alloing, JM Girardet, T Perrot- Bioscience, 2020 - portlandpress.com protein structures found in the protein databank, we tentatively attributed the changes to the Interestingly, a structure of a BolA_H from the pathogen Coxiella burnetii ligating a Co atom was solved in the frame of a structural genomic initiative for drug design, deposited in ...The coordinates of A. thaliana, B. bovis, and C. burnetii BolA proteins are from previous crystal structures (PDB entries 4PUG, 4PUH, 4PUI, 3O2E and 3TR3)
510 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
511 3o2e - Morphogenes bolA and mreB mediate the photoregulation of cellular morphology during complementary chromatic acclimation in Fremyella diplosiphon 2014 SP Singh, BL Montgomery - Molecular microbiology, 2014 - Wiley Online Library ... Hypo, gene encodes hypothetical protein. C. Putative structure of F. diplosiphon BolA (in green) modelled on the Babesia bovis BolA structure (in red, PDB:3O2E; Abendroth et al., 2011) using two independent protein structure prediction servers, ie I-TASSER and PHYRE. ...
512 3oa1 - Status of antiviral therapeutics against rabies virus and related emerging lyssaviruses 2019 V Du Pont, RK Plemper, MJ Schnell- Current opinion in virology, 2019 - Elsevier RABV drug profiles, past efforts to address the problem and inhibitor candidates identified, and examine how the rapidly expanding structural insight into RABV protein organization has illuminated novel druggable target candidates ... The solved crystal structure for the N0 binding domain is depicted in teal (PDB 3OA1). The solved crystal structure for the dimerization domain is depicted in green and pink with both top and side views...
513 3oa1 - The rabies virus phosphoprotein: novel targets and functions involved in interferon antagonism 2016 M Wachowius - 2016 - edoc.ub.uni-muenchen.de After attachment to the extracellular target structure Structural data available for the dimerization domain ( PDB ID 3L32) and C- terminal domain ( PDB ID 3OA1 ) were visualized with Cn3D software by NCBI B) Overview over the RABV P trafficking signals
514 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
515 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. ...
516 3oa3 3ngj, 3ndo Methods And Microorganisms For The Production Of 1, 3-Butanediol 2018 R Mahadevan, A Yakunin, P Gawand- US Patent App. 15, 2018 - Google Patents 2.4.). In some embodiments, DERA enzymes can be described as class I aldolases that form covalent Schiff base intermediates. In all studied structures , DERA adopts the classical eight-bladed TIM barrel fold. The oligomerisation
517 3obk - The Se S/N interactions as a possible mechanism of -aminolevulinic acid dehydratase enzyme inhibition by organoselenium compounds: a computational study 2020 PA Nogara, L Orian, JBT Rocha- Computational Toxicology, 2020 - Elsevier Figure 1. (A) The structural formula of some organoselenium compounds, (B) the 5-aminolevulinic acid (5 theory (DFT) approach, are frequently used in the study of structures , reactions, and modeling has been successfully employed to predict the 3D protein structure , which is... (HEM2_STAAR); Toxoplasma gondii: PDB (3OBK); Wolbachia: NCBI (WP_041571452.1).
518 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. ...
519 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. ...
520 3obk 3sth, 3ujh Screening for small molecule inhibitors of Toxoplasma gondii 2012 S Kortagere - Expert opinion on drug discovery, 2012 - Taylor & Francis ... A screening for protein targets in T. gondii, for which a crystal structure is available and a ...3OBK Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from T. gondii ME49 in complex with the reaction product porphobilinogenr ...
521 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 ...
522 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 ...
523 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
524 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).
525 3oc6 - Computational protein design: assessment and applications 2015 Z Li - 2015 - scholarworks.iupui.edu ... 53 xiii Page 14. Figure 3.8 Superposition of the target structures ( PDB ID 3PTE and 1B1U, cyan) ... These interactions are utilized in protein structure prediction and protein design. ... structural topology and function through evolution. Experimental techniques, such as ...
526 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).
527 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. ...
528 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
529 3oec - Biochemical Studies and Ligand-bound Structures of Biphenyl Dehydrogenase from Pandoraea pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme 2011 S Dhindwal, DN Patil, M Mohammadi? - Journal of Biological Chemistry, 2011 - ASBMB ... PDB code 1BDB and BphB B-356 are shown in black color, and other structures are shown in light colors. These PDB codes are: 2HQ1, 3OEC, 3PKO, 2UVD, 2PNF, 2WSB, 1YDE, 2WDZ, 1HDC, and 1NFR. Reactivity of BphB B-356 with Polychlorinated Biphenyls. ...
530 3oib - Unraveling cholesterol catabolism in Mycobacterium tuberculosis: the ChsE4-ChsE5 α2β2 acyl-CoA dehydrogenase initiates β-oxidation of 3-oxo-cholest-4-en-26-oyl … 2015 M Yang, R Lu, KE Guja, MF Wipperman… - ACS Infectious …, 2015 - ACS Publications ... he RMSD value between ChsE4 and 3OIB is 1.718 Å with 831 α-carbons aligned; the RMSD value between ChsE4 and 3MDE is 2.362 Å with 942 α-carbons ...
531 3oib - Identification and characterization of cholesterol metabolism related genes and gene products from Mycobacterium tuberculosis 2015 M Yang - 2015 - search.proquest.com ... Cholesterol has indispensible structural and regulatory roles in humans. ... N-terminis. C-terminus.Figure 2-1. Typical human homotetrameric ACAD structure. (a) Homotetrameric assembly of.human MCAD (PDB code: 1EGC) with four FAD molecules (yellow spheres) and four. ...
532 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
533 3oj7 - Expression, purification, crystallization and preliminary X-ray crystallographic analysis of human histidine triad nucleotide-binding protein 2 (hHINT2) 2013 R Dolot, A Wlodarczyk, GD Bujacz? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... above 15% similarity to a given hHINT2 sequence and BALBES, and five of them were used for further calculations: PDB entries 1kpf ... 404, 627-638.] ), 3oj7 (HIT family protein from Entamoeba histolytica; 40.2% similarity; Seattle Structural Genomics Center for Infectious Disease ...
534 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]
535 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. ...
536 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 ...
537 3oq8 - Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum 2016 Y Park, Y Cho, YH Lee, YW Lee, S Rhee - Journal of structural biology, 2016 - Elsevier ... The MoICL residues were selected based on the proposed structural and functional features ... In previous, unpublished work, we also observed nearly identical structural changes in Brucella melitensis ICL complexed with malonate (PDB 3OQ8). ...
538 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 ...
539 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 ...
540 3p0x - Characterisation and structural analysis of glyoxylate cycle enzymes of Teladorsagia circumcincta 2020 S Umair, C Bouchet, N Palevich, HV Simpson- Molecular and Biochemical, 2020 - Elsevier to compare the TciICL and TciMS protein sequences with deposited structures in the Protein Data Bank ( PDB ) Locations are shown of the C- and N-terminus in the predicted tertiary structure of TciICL C) and TciMS in salmon (F) within 4 of the superimposed 3P0X and 3S9Z
541 3p0x - Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2 2019 RP Bhusal, W Jiao, BXC Kwai, J Reynisson- Nature, 2019 - nature.com The structural resemblance of the Mtb ICL2 C-terminal domain to members of the GNAT observed in crystal structures of isocitrate-bound ICL1 from Brucella melitensis (Bm ICL1, PDB 3P0X ) of the active site loop are more similar to that found in the crystal structure of substrate
542 3p0x - Identification of protein-ligand binding site using machine learning and hybrid pre-processing techniques 2015 YKG Wong - 2015 - ira.lib.polyu.edu.hk ... This type is suit- able if no structural information about the target is available. Another one isstructure- ... All this information can be found from the Protein Data Bank (PDB) [6] or Protein Qua-ternary Structure file server (PQS) [7], which show the atomic coordinates and the qua- ...
543 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. ...
544 3p0x - Lifting the lid on GPCRs: the role of extracellular loops 2012 M Wheatley, D Wootten, MT Conner… - British journal of …, 2012 - Wiley Online Library ... Family A GPCRs: ECL structural aspects. ... 2RH1); B, D3R (yellow; PDB accession 3PBL); C, A2A R (orange; PDB accession 2YDO); D, CXCR4 (green; PDB accession 3OE0). ... In contrast, theECL2 of the β 2 AR possess a radically different structure comprising a short α-helix that ...
545 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 ...
546 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
547 3p10 - Identification and structural characterization of two 14-3-3 binding sites in the human peptidylarginine deiminase type VI 2012 R Rose, M Rose, C Ottmann - Journal of Structural Biology, 2012 - Elsevier ... of structures ( [Schumacher et al., 2010a], [Schumacher et al., 2010b] and [Molzan et al., 2010]) (PDB IDs: 3NKX, 3O8I, 3IQV, 3LW1, 3IQU, 3IQJ, 3P10, 3P1Q, 3P1N, 3P1R, 3P1S, 3MHR), and which only yields crystals when a peptide is bound in the binding groove of 14-3-3 ?. ...
548 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. ...
549 3p32 - Mathematical Modeling and Screening of Ligand Binding Sites in Protein using the Tetrahedral Motif Method and Double-Centroid Representation 2012 VM Reyes - 2012 - ritdml.rit.edu ... unannotated structures in PDB with unknown function to identify possible candidates that might have FMN bound to them. _ + ... Structures from the PDB for Screening using the screening procedure established for the above mathematical model for the binding site.[11] Page 19. ...
550 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. ...
551 3p3a 3hzu, 4lw8 Challenges and opportunities of automated proteinprotein docking: HDOCK server versus human predictions in CAPRI Rounds 3846 2020 Y Yan, J He, Y Feng, P Lin, H Tao- Proteins: Structure, 2020 - Wiley Online Library prediction of this dimer interface is expected. For T144, the TPC1 channel structures of mouse ( PDB ID: 6C9A) and Arabidopsis thaliana ( PDB ID: 5DQQ) were used as the templates to construct the human TPC2 channel structure ( PDB ID: 6NQ0). Despite the low sequence
552 3p4i - Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface 2012 S Chittori, H Savithri, M Murthy - BMC structural biology, 2012 - biomedcentral.com ... Crystal structures of two archeal acetate kinases, from Thermotoga maritima (PDB:2IIR, unpublished results) and Methanosarcina thermophila[15] and one from Mycobacterium avium (PDB:3P4I, unpublished results) have been determined earlier. ...
553 3p4i 4dq8 Mycobacterium tuberculosis kinases as potential drug targets: production of recombinant kinases in E. coli for functional characterization and enzyme inhibition 2015 V Lukman - 2015 - uir.unisa.ac.za ... Other mycobacterial AKs have been deposited in the Protein Data Bank (www.pdb.org), with high levels of similarity to the putative Mtb AK (M. avum, pdb 3P4I at 74.4% and M. marinum pdb 4DQ8 at 75.1%). ...
554 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.
555 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
556 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 ...
557 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
558 3p96 3km3, 3k9g Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal 2016 TC Terwilliger, G Bunkczi, LW Hung - Section D: Structural , 2016 - scripts.iucr.org ... Journal logo, STRUCTURAL BIOLOGY. ... 49-93.] ) that accounts for over 70% of depositions of experimentally phased structures in the Protein Data Bank (PDB; Berman et ... requires a specific element to be present at a limited number of sites in the macromolecular structure and the ...
559 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 ...
560 3p96 - Identification of a novel ligand binding site in phosphoserine phosphatase from the hyperthermophilic archaeon Thermococcus onnurineus 2013 TY Jung, YS Kim, BH Oh, E Woo - Proteins: Structure, Function, and Bioinformatics, 2013 - Wiley Online Library ... Flexible movement between the open structure (PDB ID: 1L8L, 1RKV, 2FEA, and 3M1Y), colored in bright orange, and closed structures (PDB ID: 1F5S, 1L7M, 1J97, 1L7P, 3P96, and 3KD3), colored in bluewhite, were analyzed by the program DynDom. ...
561 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 ...
562 3p96 - The M. tuberculosis HAD phosphatase (Rv3042c) interacts with host proteins and is inhibited by Clofazimine 2016 S Shree, AK Singh, R Saxena, H Kumar - Cellular and Molecular , 2016 - Springer ... SanyalAffiliated withBiochemistry Division, CSIR-Central Drug Research Institute; and 1 more: ,Ravishankar RamachandranAffiliated withMolecular and Structural Biology Division ... Homologymodels of MtSerB2 based on M. avium SerB (PDB code 3P96) were generated ...
563 3p96 - Targeting the Serine Pathway: A Promising Approach against Tuberculosis? 2019 M Haufroid, J Wouters- Pharmaceuticals, 2019 - mdpi.com Structural differences can occur from one specie to another, ie, human phosphoserine phosphatase is only composed of the PSP domain while of the pathway in order to inhibit the reaction in an allosteric manner (Figure 7b).... Structure of M. avium (3P96) with domain ACT-I in orange, ACT-II in blue, the linker between two ACT domains in red, PSP catalytic domain in grey, linker between PSP domain and ACT-II in green (b). ...
564 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 ...
565 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
566 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
567 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
568 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 ...
569 3pgz - Structural Diversity Based on Variability in Quaternary Association. A Case Study Involving Eubacterial and Related SSBs 2012 SM Arif, M Vijayan - Single-Stranded DNA Binding Proteins, 2012 - Springer ... structures reported in the literature and/or the coordinates of which have been deposited in the Protein Data Bank (PDB) ( 17 ) form ... in the PDB, but the results are yet to be published: 1. Thermus thermophilus (TtSSB) (PDB code 2cwa). 2. Bartonella henselae (BhSSB) (3pgz). ...
570 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
571 3pgz - Crystal Structure of a Monomeric Thiolase-Like Protein Type 1 (TLP1) from Mycobacterium smegmatis 2012 N Janardan, RK Harijan, RK Wierenga, MRN Murthy - PloS one, 2012 - dx.plos.org ... DALI search using this domain against the PDB shows structural similarities to a molybdenum binding protein (PDB id: 1H9K) [20] and a single strand DNA binding protein (PDB id: 3PGZ) (Seattle Structural Genomics Center for Infectious Disease; Unpublished). ...
572 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 ...
573 3pk0 5if3 Two enantiocomplementary Ephedrine Dehydrogenases from Arthrobacter sp. TS-15 with broad substrate specificity 2019 T Shanati, C Lockie, L Beloti, G Grogan- ACS, 2019 - ACS Publications provide a detailed insight into both the functional and structural characteristics of PseDH and EDH.. A comparison with 30 structures of SDRs from bacterial species in the PDB suggests that S143 is most commonly a small hydrophobic residue, such as G, A, or V, whereas W152 is most commonly an H, M, or L, although in SDRs from Burkholderia vietnamiensis (5IF3) and Mycobacterium smegmatis (3PK0) the residue is W
574 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
575 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) ...
576 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 ...
577 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 ...
578 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 ...
579 3py6 - Computational analysis of N-H...PI interactions and its impact on the structural stability of beta-lactamases 2014 P Lavanya, S Ramaiah, A Anbarasu - Computers in Biology and Medicine, 2014 - Elsevier ... Three dimensional structures of ?-lactamases were retrieved from Protein Data Bank (PDB) [26]. ... The PDB codes of selected 67 ?-lactamases in the dataset are as follows: ... A, 3IF6-A, 3L6N-A, 3LVZ-A, 3LY3-A, 3M2K-A, 3OPL-A, 3OZH-A, 3P09-A, 3PAE-A, 3PG4-A, 3PY6-A, 3QI0-A ...
580 3py6 - Influence of CH... O interactions on the structural stability of beta-lactamases 2013 P Lavanya, S Ramaiah, A Anbarasu - Journal of Biological Physics, 2013 - Springer ... We selected a non-redundant data set of 95 ?-lactamases from the Protein Data Bank (PDB) [23] for our ... Table 2 CHEEEO interacting residues in the active site of ?-lactamases PDB ID Active site residues ... 130 Ser 70 Ser 235 Arg 244 Met 69 Tyr 105 Val 216 Gly 236 3PY6-A Arg ...
581 3py6 - Cation-PI Interactions in beta-Lactamases: The Role in Structural Stability 2012 P Lavanya, S Ramaiah, A Anbarasu - Cell biochemistry and biophysics, 2012 - Springer ... 3PY6-A K37?Y263 -5.33 -1.41 -6.74 K231?W228 -8.02 -1.66 -9.68 2G2W-A R266?F66 -1.62 -1.06 -2.71 R259?W290 -7.01 -4.74 -11.75 K34?W60 -2.81 -0.75 -3.56 Cell Biochem Biophys 123 Page 3. Table 1 continued PDB ID Cation?p interacting residues ...
582 3q1t - Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs) 2013 Z Wang, P Yin, JS Lee, R Parasuram? - BMC Bioinformatics, 2013 - biomedcentral.com ... A structural genomics protein from Mycobacterium avium (PDB ID 3q1t) has been reported to be an enoyl-CoA hydratase (ECH), but SALSA ... There are currently over 11,000 structural genomics (SG) protein structures in the Protein Data Bank (PDB) [1] and most of them are of ...
583 3q8h - Development of Inhibitors of the 2 C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents 2014 T Masini, AKH Hirsch - Journal of medicinal chemistry, 2014 - ACS Publications ... ofhe cocrystal structure of 81 with B. pseudomallei IspF (PDB code 3Q8H, Figure 4) shows that there is no direct interaction of 81 with the catalytic Zn2+ cation, but the presence of the bicyclic aromatic ring, engaged in hydrophobic interactions, probably compensates for this lack, resulting in a strong affinity of 81 or B. pseudomallei IspF. ...
584 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
585 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.
586 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. ...
587 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. ...
588 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 ...
589 3qbp - Identification of a novel fumarase C from Streptomyces lividans TK54 as a good candidate for l-malate production 2014 RR Su, A Wang, ST Hou, P Gao, GP Zhu? - Molecular Biology Reports, 2014 - Springer ... The structure files of fumarases from Mycobacterium marinum (MmFum, PDB code: 3QBP) and Mycobacterium tuberculosis (MtFum, PDB code: 3NO9) were downloaded from the PDB web site (http://?www.?rcsb.?org/?pdb/?). Results and discussion. ...
590 3qbp 3qh8 Protein surface characterization using an invariant descriptor 2011 ZA Deeb, DA Adjeroh, BH Jiang - Journal of Biomedical Imaging, 2011 - dl.acm.org ... 1. Introduction The Protein Data Bank (http://www.pdb.org/pdb/home/ home.do) (PDB) currently has more than 3000 protein struc- tures classified as uncharacterized or as proteins of unknown function. This is about 5% of the total structures in PDB. ...
591 3qdf 3r6o, 3rr6 Crystal structures of Cg1458 reveal a catalytic lid domain and a common catalytic mechanism for the FAH family 2013 R Tingting, G Yanyan, M May, Z Wenjun? - Biochemical Journal, 2013 - biochemj.org ... Source/description, PDB ID, Resolution (?), Sequence identity (%), Aligned residues, Backbone RMSD (?). C. glutamicum/Cg1458, 4DBF, 1.90, ?, ?, ?. 4DBH, 2.00, ?, ?, ?. Mycobacterium marinum M/MMAR-1718, 3QDF, 2.05, 56.73, 245, 1.11. ...
592 3qdf 4qku, 3rr6, 4maq, 4pfz, 3r6o Crystal structures of apo and liganded 4-oxalocrotonate decarboxylase uncover a structural basis for the metal-assisted decarboxylation of a vinylogous -keto acid 2016 SL Guimares, JB Coitinho, DMA Costa, SS Arajo - Biochemistry, 2016 - ACS Publications ... Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for ... Representative tertiary and quaternary structures of enzymes from (A) Mus musculus (PDB entry 1QCN(30)) and Burkholderia cenocepacia (PDB entry 4QKU); (B) Sulfolobus solfataricus (PDB entry 2Q18(32)); (C) Mycobacterium marinum (PDB entry 3QDF(39)) ...
593 3qdf - Expression, purification, crystallization and preliminary crystallographic analysis of Cg1458: a novel oxaloacetate decarboxylase from Corynebacterium glutamicum 2011 T Ran, Y Wang, D Xu, W Wang - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2011 - scripts.iucr.org ... was collected at 1.9 ? resolution using synchrotron radiation on beamline BL17U of SSRF, Shanghai, China. Structure-solution attempts by molecular replacement were successful with PDB entries 3qdf or 2dfu as the template. ...
594 3qh4 - Identification of amino acids related to catalytic function of Sulfolobus solfataricus P1 carboxylesterase by site-directed mutagenesis and molecular modeling 2016 YH Choi, YN Lee, YJ Park, SJ Yoon, HB Lee - BMB reports, 2016 - ncbi.nlm.nih.gov ... the basis of the Protein Data Bank (PDB) databases reported previously: AfuEst (PDB code: 1jji ...esterase (1qz3), MetEst (2c7b), StoEst (3aik), Mycobacterium marinum esterase (3qh4), PcaEst(3zwq ... was created by homology modeling as the superimposed ribbon structure onto it ...
595 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 ...
596 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
597 3qh4 - Protein Engineering for Enhanced Enantioselectivity of Carboxylesterase Est924 Toward Ethyl 2-Arylpropionates 2021 X Liu, M Zhao, X Fan, Y Fu - 2021 - researchsquare.com Enhancement of the enantioselectivity of carboxylesterase A by structure -based mutagenesis. J Biotechnol Page 13. Page 13/14 PDB entry A1 A2 B1 B2 Est924 I203 A203 G208 I212 3H17 M193 V194 G198 M202 3QH4 A209 F210 A214 M218 3WJ1 F197 L198 H202 F206
598 3qh4 - Structure guided engineering of a cold active esterase expands substrate range though a stabilisation mutation that allows access to a buried water chamber 2021 N Noby, R Johnson, J Tyzack, A Embaby, H Saeed- bioRxiv, 2021 - biorxiv.org to fully open the HerE plug. LipW ( PDB 3QH4 ) (26) has two shorter residues in place PestE ( PDB 2YH2) (28) does not have the plug (Figure 2b). N211 is replaced by a of helical character than the WT suggesting a higher degree of structure for the mutant at this temperature
599 3qh4 3s4k Cytosolic lipid inclusions formed during infection by viral and bacterial pathogens 2012 M Stehr, AA Elamin, M Singh - Microbes and Infection, 2012 - Elsevier ... Furthermore the three-dimensional structures of the esterases Rv0045c (PDB 3P2M) [48], Rv1847 (PDB 3S4K), and LipW (3QH4) from M. tuberculosis have been determined, but unfortunately it is not known whether these enzymes are involved in TAG hydrolysis. 5.5. ...
600 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
601 3qh4 - Lipid Inclusions in Mycobacterial Infections 2013 M Stehr, AA Elamin, M Singh - 2013 - intechopen.com ... Furthermore the three-dimensional structures of the esterases Rv0045c (PDB 3P2M) [78], Rv1847 (PDB 3S4K), and LipW (3QH4) from M. tuberculosis have been determined, but unfortunately it is not known whether these enzymes are involved in TAG hydrolysis. 3.5. ...
602 3qh8 3sbx Deciphering common recognition principles of nucleoside mono/di and triphosphates binding in diverse proteins via structural matching of their binding sites 2017 R Bhagavat, N Srinivasan- Proteins: Structure, 2017 - Wiley Online Library One highest resolution structure was taken as the representative for each site architecture or BScID type Site type (ST), Representative PDB code, Cluster size, No ST19, 3T7M, 6, 6, L80 [0.86], D102, V82, T8 [0.71], LI/TR/OX/HY. ST20, 3QH8 , 6, 6, H86 [0.71], H219, D188, S18 [0.57
603 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
604 3qha - Structure and Activity of NADPH-Dependent Reductase Q1EQE0 from Streptomyces kanamyceticus, which Catalyses the R-Selective Reduction of an Imine Substrate 2013 M Rodr?guez-Mata, A Frank, E Wells, F Leipold? - ChemBioChem, 2013 - Wiley Online Library ... 2. For structure solution, the highest sequence homologue in the Protein Data Bank was an ... to members of the gamma-hydroxybutyrate dehydrogenase (GHBDH) family such as PDB structures 3PEF ... These are 3QHA (from Mycobacterium avium 104) and 3L6D (from P. putida ...
605 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
606 3qhd 3p0z, 3P0Z Design, synthesis, and evaluation of potential Burkholderia pseudomallei IspF inhibitors 2019 S Watkins - 2019 - commons.lib.niu.edu xvi nOe Nuclear Overhauser enhancement/nuclear Overhauser effect PDB Protein Data Bank Pf Plasmodium falciparum ppm Parts per million RST Relative saturation transfer SAR Structure activity relationship SSGCID Seattle Structural Genomics Center for Infectious Disease ... It is possible the sp2 N of the imidazole is binding to the Zn2+, as seen in the crystal structures of 88 in BpIspF (3P0Z, 3QHD).
607 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
608 3qhx 3qi6 Pharmacophore-Guided Identification of Natural Products as Potential Inhibitors of Mycobacterium ulcerans Cystathionine -Synthase MetB 2021 SK Kwofie, NNO Dolling, E Donkoh, GM Laryea, L Mosi- Computation, 2021 - mdpi.com For the study, chain A of each 3D crystal structural coordinate file was used. Two experimentally elucidated structures of CGS MetB from M. ulcerans are available. The structure with PDB ID 3QI6 is bound covalently to PLP (cofactor) and the other with PDB ID 3QHX is bound
609 3qhx - SolXplain: An Explainable Sequence-Based Protein Solubility Predictor 2019 R Mall- bioRxiv, 2019 - biorxiv.org be used as a scoring function to measure the quality of a tree structure Ht at in [13], devise a fast, greedy and iterative algorithm to identify these optimal tree structures We train our XGBoost classifier on top of physio-chemical (global), sequence and structural features extracted
610 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 ...
611 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. ...
612 3qi6 6cja Catalytic specificity of the Lactobacillus plantarum cystathionine -lyase presumed by the crystallographic analysis 2020 Y Matoba, M Noda, T Yoshida, K Oda, Y Ezumi- Scientific Reports, 2020 - nature.com The reverse transsulfuration pathway, which is composed of cystathionine -synthase (CBS) and cystathionine -lyase (CGL), plays a role to synthesize l-cysteine using l-serine and the sulfur atom in l-methionine. A plant-derived lactic acid bacterium Lactobacillus plantarum SN35N
613 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. ...
614 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. ...
615 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). ...
616 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 ...
617 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).
618 3quv - INSILICO CHARACTERIZATION OF TRANSFER RNA (M G37) METHYLTRANSFERASE IN BACTERIA, ARCHAEA AND EUKARYOTA 2011 T Srinivasan, D Sudarsanam - jbstonline.com ... TrmD, aTrm5 and eTrm5 protein was modeled based on the 3QUV-B, 2ZZN-A, and PYX1Ain respectively. ... eTrm5 three dimensional structure is not available in PDB that has distinctlystructural topology to bacterial TrmD. 4. DISCUSSION ...
619 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. ...
620 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)] ...
621 3quv - Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification 2019 SE Thomas, AJ Whitehouse, K Brown, JM Belardinelli- bioRxiv, 2019 - biorxiv.org at 1.67 and 1.48 resolution respectively ( PDB codes 6NW6 & 6NW7). The crystals belong 109 region is largely disordered, with residues 162-177 not clearly visible in the apo structure 115 of a deep trefoil knot architecture , made of three distinct untwisted loop regions
622 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
623 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
624 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
625 3qxz 3rsi, 3pk0, 5b8i, 5ji5, 4qfe, 3moy Human Missense Variation is Constrained by Domain Structure and 2017 SA MacGowan, F Madeira, T Britto-Borges - discovery.dundee.ac.uk the protein structure level. Figure 2B shows that this result extends to other protein 109 For 182 an example see Glu 295 and Ser 332 in PDB ID: 3e00 chain D.).21 These important 183 Glu370 that recent structural studies suggest is at the interface with Ubiquitin22 and so 187
626 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
627 3r0o - Metabolism of β-valine via a CoA-dependent ammonia lyase pathway 2015 M Otzen, CG Crismaru, CP Postema, HJ Wijma… - Applied microbiology …, 2015 - Springer ... to the Thermus thermophilus PaaG (35 % identity), a predicted 2, 3-dehydroadipyl-CoA hydrataseof which the structure is solved (PDB 3HRX ... searches of the protein encoded by ORF12 showedhomology to Mycobacterium avium carnitinyl-CoA hydratase (3R0O; 48 % identity ...
628 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
629 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 ...
630 3r1i - Insilico Characterization and Homology Modeling of Arabitol Dehydrogenase (ArDH) from Candida albican 2013 MW Sarwar, IB Saleem, A Ali, F Abbas - Bioinformation, 2013 - ncbi.nlm.nih.gov … used for multiple sequence alignment of ArDH with other dehydrogenases from Mycobacterium marinum (PDB Id: 3R1I), Candida parapsilosis ...
631 3r1j - Protein Similarity Networks Reveal Relationships among Sequence, Structure, and Function within the Cupin Superfamily 2013 R Uberto, EW Moomaw - PLoS One, 2013 - journals.plos.org File S1 Combined Supporting Information Files - Alpha-ketoglutarate-dependent taurine dioxygenase Mycobacterium avium 3r1j
632 3r20 - Insight from the structural molecular model of cytidylate kinase from Mycobacterium tuberculosis 2013 NK Verma, B Singh - Bioinformation, 2013 - ncbi.nlm.nih.gov ... known structure (template) of Mycobacterium smegmatis (PDB ID: 3R20) was chosen from proteindatabank (PDB) by using ... experimental structure of cytidylate kinase of Mycobacterium tuberculosis is not yet available in PDB (Protein Data Bank), comparative modeling ...
633 3r20 - Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis 2016 R Cloete, E Oppon, E Murungi - BMC , 2016 - bmcbioinformatics.biomedcentral. ... Abbreviations used: NUI- Not under investigation, PDB- Protein Data Bank, TBSGC- TB StructuralGenome ... without 3R20 used as a template while the red model consist of 3R20 used as ... EM assistedwith modelling of the protein structure and WS visually inspected the quality of ...
634 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
635 3r2v - Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome 2013 S Warren, XF Wan, G Conant, D Korkin - PloS one, 2013 - dx.plos.org ...Table 3. Coverage and sequential similarity of protein templates. Template Template subtype Template similarity, % Residues covered 3R2V (A) H3N2 93 538-720
636 3r2v - Structural templates for modeling homodimers 2013 PJ Kundrotas, IA Vakser, J Janin - Protein Science, 2013 - Wiley Online Library ... (3sb9). 37 The other four exceptions (3r2v, 3ra5, 3qlm, 4dz2) are likely to be monomers ... Science 338:1042- 1046. 4. Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide ProteinData Bank (wwPDB): ensuring a single, uniform archive of PDB data. ...
637 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).
638 3r4t - Modeling and Docking Study of GABA-AT Protein in Mycobacterium Tuberculosis-A Computational Approach 2018 R Sriroopreddy, P Raghuraman- Research Journal of, 2018 - search.proquest.com The best similarity match with the template identity of 83% ( PDB ID: 3R4T ) The secondary structure prediction was done using YASPIN server (http://zeus.few.vu.nl/).8 The result of the secondary structure prediction provides a brief idea about the folding pattern of the
639 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
640 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 ...
641 3r8c 4die, 3r20 The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor 2020 R Mega, N Nakagawa, S Kuramitsu, R Masui- PloS one, 2020 - journals.plos.org open form, CMP-bound closed form, ADP-CDP-Gd 3+ -, and CDP-bound forms at resolutions of 1.7, 2.2, 1.5, 1.6, and 1.7 , respectively (Table 1, Fig 1). Structural differences between (B) Superimposition of the overall structure of ligand-free form (gray; PDB code 3W90 ... and ligand-free form of CMPK from M. abscessus (dark gray; 3R8C). These structures were structurally aligned ... The ligand-free form of M. smegmatis CMPK (PDB code 3R20) is almost the same structure as M. abscessus CMPK.
642 3r8c 3te8 Improving ranking of models for protein complexes with side chain modeling and atomic potentials 2013 S Viswanath, DVS Ravikant? - Proteins: Structure, Function, and Bioinformatics, 2012 - Wiley Online Library ... Target PDB ID, Receptor homolog (PDB_chain): target receptor chain, Ligand homolog (PDB_chain): target ligand chain. 2xt4, 2XT2_A:B, 2XT2_A:A. 2xty, 2XTW_A:B, 2XTW_A:A. ... 3pra, 3PRB_A:B, 3PRB_A:A. 3r8c, 3R20_A:A, 3R20_A:B. 3rd6, 3Q64_A:A, 3Q64_A:B. ...
643 3r8c 4em8, 3te8 Scoring functions for protein docking and drug design 2014 S Viswanath - 2014 - repositories.lib.utexas.edu ... are also found in cell membranes, which is a hydrophobic (non-polar and water-repelling) environment. Figure 1.1 shows two complexes in the Protein Data Bank (PDB)[6, 7]. Figure 1.1 (a) is a structure of soluble complex (PDB ID 3hct) [6], which is a structure of ...
644 3r9r - Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping 2019 SE Thomas, P Collins, RH James- of the Royal, 2019 - royalsocietypublishing.org purine biosynthesis in maintaining the viability of cells and differences in the structural architecture of bacterial The crystals are similar to those of a previously determined structure of MabPurC with a monomer in the asymmetric unit (figure 1b) ( PDB 3R9R , Seattle Structural
645 3r9r - Structure-guided, target-based drug discoveryexploiting genome information from HIV to mycobacterial infections 2016 S Malhotra, SE Thomas, MB Ochoa - Postepy , 2016 - postepybiochemii.pl ... purC structure from Saccharomyces cerevisiae (PDB ID: 1OBD) and in pink is the recentapo-form crystal structure (PDB ID: 3R9R) of purC ... The modelling pipeline begins with identificationof structural homolog(s) using a sequence-structure homology recogni- tion approach ...
646 3r9r - APPLICATIONS OF SPERMINE AND DERIVATIVES THEREOF 2020 W Pan, W Zhu- US Patent App. 16/889,500, 2020 - freepatentsonline.com pneumonia (4FGR, 4FE2), Mycobacterium abscessus ATCC 19977/DSM 44196 ( 3R9R ), Thermotoga maritime On the basis of the above results, the crystal structure conformations in synthetases of Saccharormyces cerevisiae ( PDB : 2CNQ) and Escherichia coli ( PDB : 2GQS) are
647 3r9r 3lp8, 5vev Studying the mechanism and action of Purine biosynthesis enzymes in Mycobacterium Tuberculosis H37RV 2018 SJ Almehmadi - 2018 - lra.le.ac.uk Structural determination of SAICARs in M. tuberculosis and refinement, results tetraacetic acid F1 forward primer Fc calculated structure factors Fo observed structure factors Fo-Fc OD optical density ORF open reading frame PCR polymerase chain reaction PDB protein Data
648 3rd5 - In silico structural analysis and ligand-binding predictions of a few developmental stage specific-proteins during in vitro morphogenesis in Vanilla 2020 M Sultana, G Gangopadhyay- Vegetos, 2020 - Springer The crystal structure of anoxidoreductase protein (a putative uncharacterized protein from Mycobacterium paratuberculosis, PDB ID- 3RD5 ) was used as a template to predict the three dimensional model (Fig. 5e) of it. The predicted docking model (Fig
649 3rd5 - Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family 2014 NTN Tang, L Le - Evolutionary bioinformatics online, 2014 - ncbi.nlm.nih.gov ... structures within each group were compared with each other and the selected structure was the ...GROUPS, PDB CODE AND NAME OF REPRESENTATIVE STRUCTURES. ... 4, 3rd5 chain A, aputative uncharacterized oxidoreductase protein from Mycobacterium Paratuberculosis. ...
650 3rd5 - Comparatives study on sequence structure function relationship of human short-chain dehydrogenases/reductases 2013 TTN Nu - 2013 - csc.hcmiu.edu.vn ... Table 1 : PDB code and name of five representative 4. 3rd5 chain A, Retinol dehydrogenase 11...
651 3rd5 - Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW) 2019 M Jiang, H He, WP Su- Crystals, 2019 - mdpi.com It is worth mentioning that 3RD5 is a test structure with the lowest solvent content that we have successfully applied the direct method to. 4. Methodology After locating the two ligands, MJ and HH were informed that the test structure has the PDB code 4LNW
652 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. ...
653 3rd5 - Mechanistic Studies on the Light-Dependent NADPH: Protochlorophyllide Oxidoreductase and Animal Cryptochromes 2018 N Archipowa - 2018 - search.proquest.com a C15-E-anti-configuration as shown in Figure 1.4A [8]. This is followed by formation. of several thermally activated intermediates comprising structural changes of the POR. Crystal structure of the NB-protein catalytic site ( PDB : 3AEK [32]). The
654 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. ...
655 3rd5 - The tumour suppressor gene WWOX is mutated in autosomal recessive cerebellar ataxia with epilepsy and mental retardation 2013 M Mallaret, M Synofzik, J Lee, CA Sagum, M Mahajnah? - Brain, 2013 - Oxford Univ Press ... The mutated glycine 372 is located in the C-terminal part of the dehydrogenase/reductase domain of WWOX. The closest homologue of this domain with known 3D structure is 3RD5, a bacterial small dehydrogenase/reductase (pdb code 3RD5). ...
656 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 ...
657 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%).. ...
658 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 ...
659 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
660 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
661 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
662 3rih - Studies on Structure-Function Relationship and Conversion of Coenzyme Requirement in Bacterial -Keto Acid Reductases Responsible for Metabolism of 2015 R Takase - 2015 - repository.kulib.kyoto-u.ac.jp ... Data Page 5. 2 Bank ( PDB ) (www.wwpdb.org/) (40), in proportion to the progress in the field of structural biology. Structure -based biotechnology is expected to become an important part of post- structural biology. For ...
663 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 ). ...
664 3rmi 4kzp, 4gt1, 4q04 Prediction of Homodimeric Residue-residue Contacts Through Co-evolutionary and Sequence-based Analysis 2018 Y Hsieh - 2018 - edepot.wur.nl 1000 residue range, and a quick pass of the identifiers through RCSB PDB's web-based However, we do not perform any sort of structural alignment to filter out structurally similar the case that this choice biases our dataset towards a certain type of structure , therefore impacting
665 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. ...
666 3rqi - A variable active site residue influences the kinetics of response regulator phosphorylation and dephosphorylation 2016 RM Immormino, RE Silversmith, RB Bourret - Biochemistry, 2016 - ACS Publications ... reaction kinetics by altering access to the active site while not perturbing overall protein structure . ... Collectively, our biochemical and structural analyses indicate that position T+1 affects access to the ... (A) Surface representation of the E. coli CheY active site ( PDB entry 1fqw). ...
667 3rqi - A Predicted Structure for the PixD-PixE Complex Determined by Homology Modeling, Docking Simulations, and a Mutagenesis Study 2013 S Ren, R Sato, K Hasegawa, H Ohta, S Masuda - Biochemistry, 2013 - ACS Publications ... PixE Homology Modeling The amino acid sequence of PixE was obtained from the DNA DataBank of Japan (entry ... were bacterial response regulators (best 20 defined as those with the smallest E values; PDB entries 3LUF, 3N0R, 3GT7, 1QKK, 3KHT, 3RQI, 2ZQT, 2QZJ ...
668 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) ...
669 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 ...
670 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 ...
671 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
672 3rr2 - Biochemical properties of nematode< i> O</i>-acetylserine (thiol) lyase paralogs imply their distinct roles in hydrogen sulfide homeostasis 2013 R Vozdek, A Hn?zda, J Krijt, L ?er?, V Ko?ich - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2013 - Elsevier ... First, their amino acid sequences, together with sequences of OAS-TL (PDB ID: 1D6S, 1FCJ, 1O58, 1VE1, 1Y7L, 1Z7W, 2EGU, 2JC3, 2PQM, 2Q3D, 2V03 and 3RR2) and CBS (PDB ID: 1JBQ and 3PC3) were aligned using MUSCLE 3.8.31 [23]. ...
673 3rr2 - Structural characterization and functional analysis of cystathionine synthase: an enzyme involved in the reverse transsulfuration pathway of Bacillus anthracis 2017 S Devi, A Rehman, A Syed, KF Tarique- The FEBS, 2017 - Wiley Online Library Superposition of the BaCBS structure (purple) with the (A) human CBS ( PDB ID: 1M54), (B) PLP-bound OASS ( PDB ID: 2Q3B), and (C) PLP-unbound OASS ( PDB ID: 1O58) structures . (D) Structural superposition of BaCBS (purple) with PDB ID: 1OAS (yellow), PDB ID: 1VE1
674 3rr2 - Structural and biochemical analyses of< i> Microcystis aeruginosa</i> O-acetylserine sulfhydrylases reveal a negative feedback regulation of cysteine biosynthesis 2014 M Lu, BY Xu, K Zhou, W Cheng, YL Jiang? - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014 - Elsevier ... The sequences are (PDB codes in parentheses) Mycobacterium tuberculosis OASS (2Q3D), Haemophilus influenzae OASS (1Y7L), Salmonella typhimurium OASS (1OAS), Mycobacterium marinum Atcc Baa-535 OASS (3RR2), Thermotoga maritima OASS (3FCA), Arabidopsis ...
675 3rr2 - Insights into multifaceted activities of CysK for therapeutic interventions 2019 P Joshi, A Gupta, V Gupta- 3 Biotech, 2019 - Springer PDB ID (References) 3RR2 (Baugh et al A recent study where a natural A241V variant of S. flexneri CysE has unstable quaternary assembly and reduced activity, suggests transient dissociation of quaternary structure of CysE to be another regulatory mechanism for cysteine
676 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
677 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
678 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,
679 3s4k - Biosynthesis and Cellular Actions of Bioactive Natural Products 2015 S Mori - 2015 - oaktrust.library.tamu.edu The structure of AziG was determined using the molecular replacement method, with Mycobacterium tuberculosis thioesterase (PDB ID: 3S4K) as the model.
680 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 ...
681 3s4k - Polyketide Ring Expansion Mediated by a Thioesterase, CEC Domain, in Azinomycin Biosynthesis: Characterization of AziB and AziG 2016 S Mori, D Simkhada, H Zhang, MS Erb, Y Zhang - Biochemistry, 2016 - ACS Publications ... he structures of AziG were determined using the molecular replacement method, with Mycobacterium tuberculosis thioesterase (PDB entry 3S4K) as the initial model. . ...
682 3s6d - Leptospira interrogans triosephosphate isomerase: exploring the structural determinants of stability, high reaction rate and specificity. 2020 V Pareek, V Dhayabarn, H Balaram, PR Krishnaswamy- bioRxiv, 2020 - biorxiv.org Contrary to our observation for the LiTIM structure , the backbone -CO of Trp11 has previously been observed in other TIMs (eg Page 15. 15 rare example of Glu at position 94 (LiTIM numbering) is in Coccidiodes immitis ( PDB ID: 3S6D ; Figures S2 and S5B)
683 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
684 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
685 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
686 3s6l 3njb, 3p96, 3km3, 3k9g, 3men, 3oib, 3o2e Substructure determination using phase-retrieval techniques 2018 P Skubk- Acta Crystallographica Section D: Structural Biology, 2018 - scripts.iucr.org determination by PRASA has been integrated into the CRANK2 pipeline for automated structure solution from 3fki, 3gyv, 3k9g, 3km3, 3lmt, 3lmu, 3men, 3njb, 3o2e, 3oib, 3p96, 3s6l , 4us7, 4xvz the authors who kindly provided SAD data sets or deposited Bijvoet pairs in the PDB
687 3s6o - Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus 2013 VE Fadouloglou, M Kapanidou? - Acta Crystallographica Section D Biological Crystallography, 2013 - scripts.iucr.org ... These included PDB entries 1ny1 , 1w17 , 1w1a , 2c1g , 2cc0 , 2j13 , 3n2q , 3rxz , 3s6o and models produced by MODELLER as obtained through the ModBase database (Fiser & Sali, 2003 [Fiser, A. & Sali, A. (2003). Methods Enzymol. ...
688 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
689 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
690 3s99 - The evolving story of AtzT, a periplasmic binding protein 2019 ML Dennis, L Esquirol, T Nebl, J Newman- Section D: Structural, 2019 - scripts.iucr.org (2019). D75, 9951002 Page 5. cluster protein and had electron density in the binding site for a purine. Post hoc analysis of the structure and sequence showed that PDB entry 3s99 has 54% sequence identity and an rmsd of 1.2A (over $330 residues) to AtzT
691 3s99 - Evidence for an ABC-Type Riboflavin Transporter System in Pathogenic Spirochetes 2013 RK Deka, CA Brautigam, BA Biddy, WZ Liu? - mBio, 2013 - Am Soc Microbiol ... bind a small molecule between its two lobes. An adenine-binding protein from Brucella melitensis (unpublished PDB accession code 3S99; RMSD = 1.8 ? over 260 comparable C ? atoms) is also structurally similar to TP0298. ...
692 3sbx - Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales 2018 S Siddaramappa, V Viswanathan- Microbial, 2018 - ncbi.nlm.nih.gov using blastp analysis and acquired from GenBank, rast or the Protein Data Bank ( PDB ) http://espript.ibcp.fr/ESPript/ESPript/) to depict similarities and secondary structure information In this context, the structural and functional similarities between different CrtI homologues need
693 3sbx - (p) ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch 2019 YE Zhang, RL Brentsen, T Fuhrer, U Sauer, K Gerdes- Molecular cell, 2019 - Elsevier marinum showing similarity to the PpnN core domain and determined in the presence of adenosine monophosphate (AMP) ( PDB : 3SBX , Figure S3 Vibrio cholerae and Idomarina baltica, at a similar position to the phosphate of AMP in the M. marinum structure , suggesting that
694 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 ...
695 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).
696 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 ...
697 3sbx - Proteasomal Control of Cytokinin Synthesis Protects Mycobacterium tuberculosis against Nitric Oxide 2015 MI Samanovic, S Tu, O Novák, LM Iyer, FE McAllister… - Molecular cell, 2015 - Elsevier ... The crystal structure of the Rv1205 ortholog in the close M. tuberculosis relative Mycobacteriummarinum (M. marinum) was previously crystallized (Protein Data Bank [PDB] ID: 3SBX) in aneffort by the Seattle Structural Genomics Center for Infectious Disease ...
698 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
699 3sbx - A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis 2017 R Bhagavat, HB Kim, CY Kim, TC Terwilliger- Scientific reports, 2017 - nature.com a given ligand recognition, and (d) sensitive methods are required to compare structural motifs against binding sites 33 and combine them into a workflow to obtain structure -based function a large-scale analysis of 4,766 ATP and other NTP binding proteins from PDB and have
700 3sbx 3qh8 Deciphering common recognition principles of nucleoside mono/di/and triphosphates binding in diverse proteins via structural matching of their binding sites 2017 R Bhagavat, N Srinivasan - Proteins: Structure, , 2017 - Wiley Online Library ... The super-types are S1) 3CYI, 3HYO, 2ZKJ, 3QUR, 3SBX , 3PNL and 2QV7; S2) 3T7M, 3L31, 3EVD, 3QXH, 3H5N and 2B56; ... classification of this type groups the set of known NTP binding sites in PDB , which are more ... PROTEINS: Structure , Function, and Bioinformatics ...
701 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
702 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
703 3sdo - Crystal structure of dibenzothiophene sulfone monooxygenase BdsA from Bacillus subtilis WUS2B 2017 M Okai, WC Lee, LJ Guan, T Ohshiro - Proteins: Structure, , 2017 - Wiley Online Library ... Overall structure. ... BdsA also shows structural similarities with the following proteins: putativemonooxygenase Ytnj (PDB ID: 1TVL; Q-score 0.60, not published), nitrilotriacetatemonooxygenase NmoA (PDB ID: 3SDO; Q-score 0.57, not published), EDTA monooxygenase ...
704 3sdo - On the diversity of F420-dependent oxidoreductases: a sequence-and structure-based classification 2020 ML Mascotti, MJ Ayub, M Fraaije- bioRxiv, 2020 - biorxiv.org monooxygenase (NTA_MO, PDB : 3sdo ), as well as the well-known bacterial FMN- dependent luciferases (eg.: LuxB, PDB : 1luc) [28]. The topology suggests that cofactor vary considerably in structure and function, and comprise the F420H2-NADP+ oxidoreductases
705 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 ...
706 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 ...
707 3sdo - A Comprehensive Computational Analysis of Mycobacterium Genomes Pinpoints the Genes Co-occurring with YczE, a Membrane Protein Coding Gene 2017 T Milano, S Angelaccio, A Tramonti, ML di Salvo- Interdisciplinary, 2017 - Springer Clustal Omega multiple sequence alignment between the “luciferase-like” cluster sequences and a set of PDB structures detected by Phyre2 and/or HHpred. Sequence ids refer to Table 3 while PDB codes indicate: 3SDO|A, the chain A of nitrilotriacetate monooxygenase from Burkholderia pseudomallei
708 3sdo - Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the 4S Desulfurization Pathway 2018 T Su, J Su, S Liu, C Zhang, J He, Y Huang- Frontiers in, 2018 - frontiersin.org This work combined with our previous structure of DszC provides a systematic structural basis for the The native BdsA structure was resolved by molecular replacement using Phaser from the CCP4 suit of programs (Winn et al., 2011) with LadA ( PDB entry 3B9N) as the
709 3sdo - Structural and biochemical characterization of EDTA monooxygenase and its physical interaction with a partner flavin reductase 2016 SY Jun, KM Lewis, B Youn, L Xun - Molecular , 2016 - Wiley Online Library ... E. Open (green) and closed (cyan) form lid domains are aligned to show conservation of secondary structure of both ... Structural homologues of EmoA. ... to EmoA showed that the highest match was NTA monooxygenase (NmoA) from Burkholderia pseudomallei ( PDB : 3SDO ) with ...
710 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 ...
711 3sds - Estructura - funcion - especificidad en el ambito de las transcarbamilasas: la putrescina transcarbamilasa 2012 P Ilacqua, L Mariano - 2012 - rodrigo.uv.es ... PCR: Reacci?n en cadena de la polimerasa (Polymerase Chain Reaction) PEG: Polietil?n glicol pfOTC: L-ornitina transcarbamilasa de Pyrococcus furiosus PDB: Banco de datos de prote?nas (Protein Data Bank) PTC: Putrescina transcarbamilasa Page 13. ...
712 3sdw - Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of Streptococcal isomerase and … 2015 Y Maruyama, S Oiki, R Takase, B Mikami… - Journal of Biological …, 2015 - ASBMB ... Owing to the high sequence identity, the overall structure of SagDhuI was highly similar to threegroup I-protein structures from S. pneumoniae (PDB code 2PPW), Novosphingobium ... In contrast,group II proteins (PDB codes 1NN4, 3K8C, 3HEE, and 3SDW), which consist of ...
713 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)
714 3si9 3qfe Dihydrodipicolinate synthase is absent in fungi 2018 S Desbois, UP John, MA Perugini- Biochimie, 2018 - Elsevier Bacillus clausii, 3E96, Bartonella henselae, 3SI9 , [41] 2C) compared to the head-to-head architecture observed for bacterial tetramers (Fig. 2B). Recently, a crystal structure of a putative fungal DHDPS ( PDB ID: 3QFE) has been deposited in the Protein Data Bank ( PDB ) (Fig
715 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
716 3slg 3i3f, 3dah, 3inn, 3hm0, 4pca, 5udf, 4q1t, 5w15, 3ld9, 4ghk, 5kak, 3l0g, 4lgv, 5bq2, 3t3w, 4lgo, 5dle, 4dz4, 3tk8, 3swo 5.1 Creation of Homo Multimer Protein Complex Dataset 2018 P Kangueane, C Nilofer- Protein-Protein and Domain-Domain Interactions - Springer 3LYU, 3M1R, 3MBH, 3MQ1, 3MW9, 3N2N, 3NWY, 3OVG, 3OZB, 3PW3, 3SBA, 3SLG , 3T3W, 3T94 Distribution of homo multimer protein complex structures at the protein data bank ( PDB ) 5.3 Structure of a homo trimer glycosidase (1AM7) from enterobacteria phage lambda is
717 3slg - Human UDP-?-d-xylose Synthase and Escherichia coli ArnA Conserve a Conformational Shunt That Controls Whether Xylose or 4-Keto-Xylose Is Produced 2012 SJ Polizzi, RM Walsh Jr, WB Peeples, JM Lim? - Biochemistry, 2012 - ACS Publications ... Recently, the Seattle Structural Genomics Center for Infectious Disease deposited the atomic coordinates of an annotated UGA decarboxylase from Burkholderia pseudomallei (PDB entry3SLG) which conserves the same proline packing surface associated with the ...
718 3sth - Molecular Adaptations in Extremely Halophilic Protists 2018 T Harding - 2018 - dalspace.library.dal.ca proteins compared to the templates used to model the tertiary structures , as a of proteins and alteration of transcriptional programs, leading to modification of cell structure properties like open reading-frame OTU operational taxonomic unit P2XR P2X receptor PDB Protein Data
719 3sth - Deciphering the mechanism and function of stage-specific protein association with the membrane cytoskeleton of Toxoplasma gondii 2017 R Dubey - 2017 - search.proquest.com Crystal structure data of TgGAPDH1 Crystal structure data collection and refinement statistics of Toxoplasma GAPDH1, PDB code 3STH Crystallographic structures of the seven selected GAPDH proteins are solved and deposited in PDB . 62 Structure of TgGAPDH1 protein
720 3svk - Structure of Mycobacterial beta-Oxidation Trifunctional Enzyme Reveals Its Altered Assembly and Putative Substrate Channeling Pathway 2013 R Venkatesan, RK Wierenga - ACS chemical biology, 2013 - ACS Publications ... From sequence alignments it is also found that the Mycobacterium avium thiolase FadA1, whose crystal structure (PDB id: 3SVK) has been deposited recently, has the same unique sequence features as mtTFE-?. This gene ...
721 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...
722 3sw5 3fq3 Effect of Structure Variations in the Inter-subunit Contact Zone on the Activity and Allosteric Regulation of Inorganic Pyrophosphatase from Mycobacterium tuberculosis 2020 RS Romanov, SA Kurilova, AA Baykov- Biochemistry (Moscow, 2020 - Springer of Ec PPase [15, 16], and bound L malate was found in the crystal struc ture of PPase from Bartonella henselae ( PDB ID 3SW5 ) Furthermore, modification of the subunit contact zones does not change the oligomeric structure of Mt PPase, but makes it less compact, as shown
723 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 ...
724 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 ...
725 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).
726 3swt - Non-Heme Iron Oxygenases: An Investigation of the Protein Ligand Effects on the Chemical Reactivity in MiaE and Cysteamine Dioxygenases 2019 P Palacios - 2019 - rc.library.uta.edu enzyme toluene monooxygenase in Figure 1.1 (panel B).14 The structural frame of the non-heme iron Figure 1.2 X-ray crystal structure of the Fe(II)/-ketoglutarate dependent enzyme TauD from Myobacterium marinum ( PDB : 3SWT )22 Page 22. 10
727 3swt - Antibiotics Targeting Tuberculosis: Biosynthesis of A-102395 and Discovery of Novel Actinomycins 2015 W Cai - 2015 - uknowledge.uky.edu ... Interestingly, Cpr19 was a monomer instead of a dimer as TauD (fig 2.3.11C,PDB ID:3SWT(110)), its closest homology, suggesting that this enzyme has a distinct three dimension structure compared with other αKG:taurine dioxygenase ...
728 3t7c 3s55 Structural studies on M. tuberculosis decaprenyl phosphoryl--D-ribose epimerase-2 enzyme involved in cell wall biogenesis 2020 SP Gangwar, A Bandyopadhyay, AK Saxena- bioRxiv, 2020 - biorxiv.org The MtbDprE2 structure was aligned with structures of PDB database using TM- structural alignment program of I-TASSER server, which yielded ten closest structural homologs (as coverage=97.2% [54] (vi) PDB - 3t7c , identity=13.3%, coverage=97.2% [55] (vii) PDB -1ipe
729 3t7c 3pgx Identification of Genes Involved in IN VIVO Virulence of Mycobacterium Fortuitum as Potential Drug Target 2020 R Srivastava - 2020 - ir.juit.ac.in acidic, hypoxic and detergent stress conditions. Structural and functional characterization of most potent ORF Mfsdr was done using in silico approaches. MfSdr was predicted to be acid synthesis. Secondary structure of MfSdr generated using Robetta server showed presence
730 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. ...
731 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
732 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 ...
733 3tcq - Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40 2016 MU Mirza, N Ikram - International Journal of Molecular Sciences, 2016 - mdpi.com ... We have identified VP40 assemblies in a filamentous structure and have shown that disruption of these structures halts viral egress... The homology-based search inferred that the 3D coordinate crystal structure of the Reston Ebola virus RNA binding domain (PDB ID: 3KS4), in addition to the crystal structure of the Sudan Ebola virus matrix protein VP40 (PDB ID: 3TCQ), were the best hits based on query coverage ...
734 3tcq - Targeting ebola virus VP40 protein through novel inhibitors: exploring the structural and dynamic perspectives on molecular landscapes 2021 S Khan, Z Fakhar, A Ahmad- Journal of Molecular Modeling, 2021 - Springer of novel antiviral drugs. Computational methods. Structural modelling. The X-ray crystallographic structure of VP40 protein ( PDB Code: 3TCQ ) [12] was retrieved from the Protein Data Bank (www.rcsb.org). The structure was prepared
735 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
736 3tde 3iml, 3s82, 3rv2 Toward an Enzyme-coupled, Bioorthogonal Platform for Methyltransferases: Probing the Specificity of Methionine Adenosyltransferases 2019 TD Huber - 2019 - uknowledge.uky.edu 4.4.5 Protein crystallization, data collection, and structure refinement ..... 105 reported similar promiscuity for the archael Sulfolobus solfataricus MAT (sMAT) and, notably, the corresponding first structural elucidation for a thermostable MAT (sMAT, PDB ID 4HPV)
737 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
738 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
739 3tf6 - DLSCORE: A Deep Learning Model for Predicting Protein-Ligand Binding Affinities 2018 M Hassan, DC Mogollon, O Fuentes, S Sirimulla - 2018 - .s3.amazonaws.com In designing DLSCORE architecture , we divided the entire method into two parts 2 PDB IDs 4rqv, 4tkb, 1met, 5c5t, 3p8p, 2iuz, 4kfq, 3ifl, 4p6c, 1oyt, 4ibg, 3uri, 3t01, 1o5e, 3qgy, 3kgu, 2h21, 3agl, 3n7a, 1qkt, 1o2j, 1azm, 1afk, 1g54, 3nu3, 2yhw, 4mme, 2f94, 3vha, 3tf6 , 2pvj, 1fkb
740 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)
741 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 ...
742 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
743 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
744 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. ...
745 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. ...
746 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) ...
747 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
748 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
749 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. ...
750 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
751 3tsc - System and method for generating detection of hidden relatedness between proteins via a protein connectivity network 2015 Z Frenkel - US Patent App. 15/310,401, 2015 - Google Patents ... The 20-amino acid fragments are derived from proteins with Protein Data Bank (PDB) codes 3tsc (chain A, starting position ALA 93) and lyxm (chain A, starting position ASP 96). These proteins have similar fold, and the RMSD (root-mean-square-deviation) function between the structures of the fragments is 0.85A, meaning that the structures are very similar, as shown in FIG. 4 ...
752 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
753 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
754 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. ...
755 3tzs - Plasmonic biosensors with built-in artificial antibodies 2016 S Singamaneni, L Tian, KK Liu, A Abbas- US Patent App. 15, 2016 - Google Patents organic silane monomers are functionalized prior to polymerizing the functional monomers onto the template molecule-nanostructure core structure 6.8, MW=64.5 kDa) or 0.5 mg/mL recombinant human neutrophil gelatinase-associated lipocalin (NGAL; pdb ID: 3TZS , Ip=8.9
756 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 ...
757 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.
758 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 ...
759 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. ...
760 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
761 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 ...
762 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 ...
763 3u0d - Acute phase 1-acid glycoprotein as a siderophore-capturing component of the human plasma: A molecular modeling study 2021 SA Samsonov, F Zsila, M Maszota-Zieleniak- Journal of Molecular, 2021 - Elsevier JavaScript is disabled on your browser. Please enable JavaScript to use all the features on this page. Skip to main content Skip to article
764 3u0d - The structure of the bacterial ironcatecholate transporter Fiu suggests that it imports substrates via a two-step mechanism 2019 R Grinter, T Lithgow- Journal of Biological Chemistry, 2019 - ASBMB TBDTs are highly divergent in sequence but share a common structural architecture , consisting of a 22 The structure of Fiu consists of a 22-stranded transmembrane -barrel characteristic of the DALI web server (37) identified PiuA from Acinetobacter baumannii ( PDB code 5FP1
765 3u0g - An in silico strategy for identification of novel drug targets against Plasmodium falciparum 2017 S Rout, NP Patra, RK Mahapatra - Parasitology Research, 2017 - Springer ... structure of our target protein was constructed taking multiple templates into account, namely, 1WRV (chain B), 3U0G (chain A), 1IYE (chain A), and 5E25 (chain A). The structural similarity between first template ( PDB ID 1WRV) and the modeled structure is 0.548 ...
766 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
767 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).
768 3u0g - A Novel highly thermostable branched-chain amino acid aminotransferase from the crenarchaeon Vulcanisaeta moutnovskia 2017 TN Stekhanova, AL Rakitin, AV Mardanov - Enzyme and Microbial , 2017 - Elsevier ... The first X-ray diffraction structure of BCATs, namely, the structure of BCAT ... The search for close homologues of VMUT0738 using BLAST showed the highest levels of identity with hypothetical BCATs from other members of the genera Vulcanisaeta … The homologues with known structures were TUZN1299 from T. uzoniensis (PDB ID 5CE8, 54% identity, query cover 94%), putative BCAT from Burkholderia pseudomallei (PDB ID 3U0G, 47% identity, query cover 94% ...
769 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
770 3u0g 4tvi, 4m0j Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold 2016 T Pavkov-Keller, GA Strohmeier, M Diepold- Scientific reports, 2016 - nature.com from Mycobacterium smegmatis 48 , 3UYY from Deionococcus radiodurans 49 , 3U0G from Burkholderia Crystallographic data processing and structure refinement statistics are presented in Table 4 confirmed function are D-amino acid aminotransferases (eg PDB -code: 1DAA
771 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 ...
772 3u40 - Insights into Phosphate Cooperativity and Influence of Substrate Modifications on Binding and Catalysis of Hexameric Purine Nucleoside Phosphorylases 2012 PO de Giuseppe, NH Martins, AN Meza? - PloS one, 2012 - dx.plos.org ... Structural superposition of BsPNP233-Ado (magenta carbon atoms), B. cereus adenosine phosphorylase (BcAdoP)-Ado-SO 4 (green carbon atoms, PDB code 3UAW [52]) and Entamoeba histolytica PNP-Ado (cyan carbon atoms, PDB code 3U40 [55]) complexes. ...
773 3u5w - The crystal structure of Rv2991 from Mycobacterium tuberculosis: An F420 binding protein with unknown function 2019 S Benini, A Haouz, F Proux, P Alzari- Journal of structural biology, 2019 - Elsevier from M. tuberculosis in complex with F 420 (Ahmed et al., 2016); 3U5W uncharacterized protein of secondary structural elements of the query (Rv2991) that match the target structure by the sequence similarity search by BLASTp when Rv2991was compared to the whole PDB
774 3uam - Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region 2019 R Arora, P Bharval, S Sarswati, TZ Sen- Journal of Molecular, 2019 - Elsevier pdb ) id: 2vtc, 2yet, 3zud, 4b5q, 4eir, 4qi8, 5acf, 5aci, 5acj, 5foh, 5tkf, 5tkg, 5tkh, and 5tki) and 10 structures in AA10 ( pdb id: 2bem, 3uam , 4ow5, 4oy6 MSF correlation value of 0.58 or higher (Table 1). In the case of AA11 and AA13 there was only one structure , 4mah and 5t7j
775 3uam - Computational Studies on Substrate Specificity in Lytic Polysaccharide Monooxygenases 2018 R Arora, RM Yennamalli - 2018 - ir.juit.ac.in 4ALS, 4ALT), Burkholderia pseudomallei CBM33 ( PDB ID: 3UAM ) [10], Bacillus coelicolor CBM2 ( PDB ID: 4OY7), Cellvibrio japonicas CBP33 ( PDB ID: 5FJQ). Page 17. 3 1.5 LPMO and substrate interactions Due to the binding of copper LPMO structure gets stabilized
776 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)
777 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
778 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 ...
779 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 ...
780 3uam - Structural Dynamics of Lytic PolysaccHaride Monooxygenase 2017 P Bharval, S Sarswati, RM Yennamalli - 2017 - 122.252.232.85 (a) For AA9 the reference structure is 2bem, (b)For AA10 the reference structure is 2bem (c) For AA11 the reference structure is 4MAH PDB ID RMSD 2BEN 0.303 2LHS 1.273 2XWX 0.491 2YOW 0.445 2YOX 0.474 2YOY 0.440 3UAM 0.700 4A02 0.880 4ALC 0.673
781 3uam - Comparative study of two chitin-active and two cellulose-active AA10-type lytic polysaccharide monooxygenases 2014 Z Forsberg, ?K R?hr, S Mekasha, KK Andersson? - Biochemistry, 2014 - ACS Publications ... Structural Sequence Alignment PyMod(27) was used to make a structure-based sequence alignment(28) of five AA10-type LPMOs with known structures: EfAA10A (PDB entry 4A02), BpAA10A (PDB entry 3UAM), VcAA10B (PDB entry 2XWX), BaAA10A (PDB entry 2YOX), and ...
782 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
783 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. ...
784 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 ...
785 3uam - Improving extracellular production of Serratia marcescens lytic polysaccharide monooxygenase CBP21 and Aeromonas veronii B565 chitinase Chi92 in 2017 Y Yang, J Li, X Liu, X Pan, J Hou, C Ran, Z Zhou - AMB Express, 2017 - Springer ... 2012), Chitin Binding Domain from Burkholderia pseudomallei ( PDB ID: 3UAM ) and CBP ... PubMedCentralGoogle Scholar. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and ...
786 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 )
787 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
788 3uam - Structural Basis for Substrate Targeting and Catalysis by Fungal Polysaccharide Monooxygenases 2012 X Li, WT Beeson, CM Phillips, MA Marletta, JHD Cate - Structure, 2012 - Elsevier ... database (Protein Data Bank [PDB]) contains crystal structures of three CBM33 members, including S. marcescens CBP21 (PDB entry 2BEM) (Vaaje-Kolstad et al., 2005) and two other CBM33s (from Burkholderia pseudomallei and Vibrio cholera, PDB entries 3UAM and 2XWX ...
789 3uam - X-ray structure and function studies of key enzymes for biomass conversion: GH6 cellobiohydrolases and GH61 lytic polysaccharide monooxygenases (LPMO) 2013 M Wu - 2013 - core.kmi.open.ac.uk ... crassa Pch/P. chrysosporium Phanerochaete chrysosporium PDB Protein Data Bank PEG Polyethylene ... faecalis CBM33 (PDBcode 4A02)(Vaaje-Kolstad et al., 2012); PDB code 4ALC ... 4ALE, 4ALO, 4ALR, 4ALS, 4ALT) and Burkholderia pseudomallei CBM33 (PDBcode 3UAM). ...
790 3uam - Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the basidiomycota fungus Phanerochaete chrysosporium 2013 M Wu, GT Beckham, AM Larsson, T Ishida? - Journal of Biological Chemistry, 2013 - ASBMB ... date, there are five LPMO structures from five different fungal GH61s available: H. jecorina GH61B (Protein Data Bank (PDB) code 2VTC ... PDB code 2XWX) (17), Enterococcus faecalis CBM33 (PDB code 4A02) (18), and Burkholderia pseudomallei CBM33 (PDB code 3UAM ...
791 3ue9 - Purification, crystallization and preliminary X-ray analysis of adenylosuccinate synthetase from the fungal pathogen Cryptococcus neoformans 2013 RD Blundell, SJ Williams, CA Morrow? - Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... Zhou, S. Peterson, W. Anderson & A. Joachimiak, unpublished work), Campylobacter jejuni (43% identity; PDB entry 3r7t ; Center for Structural Genomics of Infectious Diseases, unpublished work) and Burkholderia thailandensis (40% identity; PDB entry 3ue9 ; Seattle Structural ...
792 3ue9 - Disruption of de novo ATP biosynthesis abolishes virulence in Cryptococcus neoformans 2016 R Blundell - 2016 - espace.library.uq.edu.au ... pioneered the concept of rational drug design (28) which involves the use of metabolic, genetica nd structural studies to identify potential targets, followed by the directed search ... AdSS has been purified and characterized from several sources ... Crystal structures are also available for the proteins from Homo sapiens (54%, PDB ID: 2V40); Mus musculus (54%, (50, 99)) ... and Burkholderia thailandensis (40%, PDB ID: 3UE9);. ...
793 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 ...
794 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. ...
795 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. ...
796 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
797 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 ...
798 3ujh - Evidence for Positive Selection within the PgiC1 Locus in the Grass Festuca ovina 2015 Y Li, B Canbäck, T Johansson, A Tunlid, HC Prentice - 2015 - dx.plos.org ... 0.45 Å root-mean-square deviations for the backbone atoms from the template Toxoplasma 3ujh.pdb structure. ... of the candidate sites in the homology-modeled PGIC1 3-D structure, it can ...For comparative purposes, the 3-D protein structural locations of the PGI amino acid sites ...
799 3ujh - When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina 2020 Y Li, S Mohanty, D Nilsson, B Hansson, K Mao- Scientific reports, 2020 - nature.com F. ovina. Using simulated native-state ensembles, we examine the structural properties and binding tightness of the dimers. In addition, we investigate their ability to withstand dissociation when pulled by a force. Our results
800 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
801 3uk1 3upt Développement de biocapteurs ampérométriques pour la détermination de l'activité de la transcétolase et pour la détection d'inhibiteurs de cette enzyme 2013 N Touisni - 2013 - tel.archives-ouvertes.fr ... I.1.1.2. Structures tridimensionnelles des transcétolases ..... 11 ... biomolécules dans unematrice hôte apparait comme une méthode assez efficace tout en veillant à maintenirla structure de la biomolécule et son accessibilité par les substrats. ...
802 3uk1 3upt High-resolution structures of Lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate 2015 P Lukacik, CMC Lobley, M Bumann - Section F: Structural , 2015 - scripts.iucr.org ... In this work, we present high-resolution crystal structures of the L. salivarius UCC118 Tkt protein(LsTktA) in the presence and absence ... Burkholderia thailandensis (PDB entry 3uk1 ), B. pseudomallei (PDB entry 3upt ), ...
803 3und - Structure of 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase from Pseudomonas aeruginosa 2013 SK Nelson, A Kelleher, G Robinson? - Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2013 - scripts.iucr.org ... Biochemistry, 40, 6326-6334.] ), with 69% sequence similarity, Burkholderia pseudomallei (PDB entry 3und ; Seattle Structural Genomics Center for Infectious Disease, unpublished work), with 64% sequence identity, and Aquifex aeolicus (PDB entry 1fwt ; Ackerman & Gatti ...
804 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 ...
805 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.
806 3uqb - To fuse or not to fuse: What is your purpose? 2013 MR Bell, MJ Engleka, A Malik, JE Strickler - Protein Science, 2013 - Wiley Online Library ... The protein was crystallized and the structure determined to 1.9Å resolution with SUMO stillattached (labeled). (PDB ID 3UQB, Fox III, Abendroth, Staker, and Stewart, Seattle StructuralGenomics Center for Infectious Disease, deposited Nov. 2011). ...
807 3uw1 4em8, 3u7j Identificao in silico de potenciais inibidores da ribose 5-fosfato isomerase de Trypanosoma cruzi 2017 VVS Castilho - 2017 - arca.fiocruz.br In this study, novel potential inhibitors were proposed for the Rpi of T. cruzi (TcRpi) based on a computer-aided approach, including structure -based and ligand-based pharmacophore modeling ativo da estrutura cristalogrfica TcRpiB ( PDB 3K7S) .... 70
808 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
809 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 ...
810 3uw3 - Molecular Docking and Dynamics Simulation of Vibrio anguillarum Aspartate Semialdehyde Dehydrogenase with Natural Product Caulerpin 2016 P Aiya Subramani, R Mahendran - Letters in Drug , 2016 - ingentaconnect.com A MGGEYLSAFTVGDQLLWGAAEPLRRMLRILLDK ... 7). Further structuralchar- acterisation needs to be done ... middle is due to an unfavourable secondary loop structure. ...
811 3v2i 4f3y, 4dz4 A Computational Biology Approach in Function Annotation to Enzymes 2018 M Ljubijankic- Southeast Europe Journal of Soft Computing, 2018 - scjournal.ius.edu.ba 3.5.3.1 2Q47 3.1.1.3 3.1.3.48 3SF8 3.1.6. 3.4.-.- 3V2I 3.4.19.12 3.1.1.29 is observed in the example of the survival protein E (SurE) from Thermotogamaritima ( PDB ID 1ilv). Zhang and colleagues (2001) determined the crystal structure of this protein and in their work, described it
812 3v2i - Small Molecule Docking Supports Broad and Narrow Spectrum Potential for the Inhibition of the Novel Antibiotic Target Bacterial Pth1 2016 PP Ferguson, WB Holloway, WN Setzer, H McFeeters - Antibiotics, 2016 - mdpi.com ... were obtained from the Protein Data Bank and each structure was analyzed for ... The Pth1 setincluded eight bacterial structures: Escherichia coli (PDB 2PTH) [11 ... aeruginosa (4FYJ) [14],Francisella tularensis (3NEA) [15], Burkholderia thailandensis (3V2I) [31], Acinetobacter ...
813 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 ...
814 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.
815 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
816 3v7o 5dvw Strategies for the Development of Small Molecule Inhibitors of Ebola Viral Infection 2016 S Pleko, Podlipnik - Ebola, 2016 - intechopen.com ... 2. Structure and action of Ebola virus. ... PDB structures: 2i8b, 3v7o, 5dvw, Target basic patcharound LYS 180 to inhibit the activation of transcription. ... PDB structures: 3vne, 3vnf, 4d9o,4m0q, 4or8, 4u2x, Inhibition of VP24 binding to karyopherin. ...
817 3v7o 5dvw The Ebola virus VP30-NP interaction Is a regulator of viral RNA synthesis 2016 RN Kirchdoerfer, CL Moyer, DM Abelson - PLoS , 2016 - journals.plos.org ... the interactions of Ebola, Sudan and Marburg virus VP30 with NP using in vitro biochemistry,structural biology and cell ... here, we further compared our structures to the Reston ebolavirus(RESTV) VP30 CTD (3V7O.pdb [12]) and a more recently determined structure of the ...
818 3v7o - Ebola virus VP30 and nucleoprotein interactions modulate viral RNA synthesis 2017 W Xu, P Luthra, C Wu, J Batra, DW Leung- Nature, 2017 - ncbi.nlm.nih.gov ... resolution data crystal forms were solved by molecular replacement using the Reston virus VP30 structure ( PDB 3V7O ) as the ... Comparison of the eVP30 structure for residues 142266 between VP30-bound and -free show limited structural changes (Supplementary Fig ...
819 3v7o - Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses 2016 M Pappalardo, M Juli, MJ Howard, JS Rossman- Scientific reports, 2016 - nature.com ... of both Ebola virus ( PDB structure 2I8B) and Reston virus ( PDB structure 3V7O ) VP30 are ... Structural data are available for both the Ebola virus and Reston virus VP35 ... These structures are highly conserved, however functional studies have demonstrated that Reston virus VP35 ...
820 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
821 3v7o 3tcq Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions 2014 S Chakraborty, B Rao, B Asgeirsson… - …, 2014 - f1000research.com ... 1EBO,2EBO,3VE0,3CSY.. 2I8B,3V7O 3FKE,3L25,4LG2,4IBK... ... A PDB database search usingthe keyword 'Ebola' generate 146 single chained proteins, which were analyzed using DefineSecondary Structure of Proteins, resulting in 758 alpha helices (ALPHA.zip). ...
822 3v7o 4g50 Design of an expression system to enhance MBP-mediated crystallization 2017 T Jin, W Chuenchor, J Jiang, J Cheng, Y Li - Scientific , 2017 - ncbi.nlm.nih.gov ... 25 , GST 26 , TRX 27 , green fluorescent protein (GFP) 28 ,29 , SUMO (pdb: 3V7O and 4G50 ...platform is increasingly appreciated 38 ,39 , the optimal sequence, length, and structure of the ...The death domain superfamily is a structural motif found in many proteins that are involved ...
823 3v7o 5dvw Crystal structure of the Mngl virus VP30 C-terminal domain 2020 S Dong, K Wen, H Chu, H Li, Q Yu, C Wang- and Biophysical Research, 2020 - Elsevier VP30 CTD dimers formed from adjacent crystallographic asymmetric units with those of MARV ( PDB code: 5T3W), RESTV ( PDB code: 3V7O ) and EBOV ( PDB code: 5T3T) In this study, we determined the crystal structure of MLAV VP30 CTD monomer at 1.4 resolution
824 3v7o - Molecular Docking Studies of E-Bola Virus Protein VP30 2016 UPA Shaikh, YN Joshi - 2016 - ijsrst.com ... III. RESULT AND DISCUSSION 1. Homology Modeling and Validation: PDB id3V7O (Crystal structure of the C terminus domain of Ebola virus) was selectedas template with 37.50% sequence identity to query sequence. ...
825 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
826 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 ...
827 3v9o 3urr Flexible backbone assembly and refinement of symmetrical homomeric complexes 2018 SSR Burman, RA Yovanno, JJ Gray- bioRxiv, 2018 - biorxiv.org For local docking, specific symmetry definitions can be recapitulated from a PDB file of a complex About 22% of all structures are unfavorable, and all but one near-native (less than 5 number of inter-chain atom-atom clashes is 50.6, compared to 21 in the native structure
828 3vab - Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis 2016 MG Peverelli, TPS da Costa, N Kirby - Journal of Biological , 2016 - ASBMB ... and 1TUF) (9), Aquifex aeolicus (PDB code 2P3E), and Brucella melitensis (PDB code 3VAB)show that ... both a dimer (PDB codes 1HKW and 1HKV) (7) and a tetramer (PDB code 2O0T ... arethe results of earlier studies aimed at characterizing the quaternary structure of DAPDC ...
829 3vab - The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate 2020 VA Bielinski, JK Brunson, A Ghosh, MA Moosburner- bioRxiv, 2020 - biorxiv.org in the active site. The structure underscores features unique to the PtLYSA clan of DAPDC and provides structural insight into the determinants responsible for the substrate-promiscuity observed in PtLYSA. ... Akin to protomer 2 of PtLYSA, this segment is not included in the structures of DAPDC from Aquifex aeolicus (PDB 2P3E) and Brucella melitensis (PDB 3VAB).
830 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
831 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 ...
832 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 ...
833 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
834 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 ...
835 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 ...
836 4di1 3moy Structural and bioinformatic analysis of ethylmalonyl-CoA decarboxylase 2015 RL Roberts - 2015 - search.proquest.com ... is the murine methylmalonyl-CoA decarboxylase trimer (PDB code: 1ef8), bottom right is thehuman AUH protein hexamer (PDB code: 1hzd). ... Having a 3D structure of EMCD could allowresearchers to probe the active site and intelligently design structural perturbations to ...
837 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
838 4djt - Existuj sekvenn determinanty funkn divergence GTPz? 2017 O Kraus - 2017 - dspace.cuni.cz ... responsible for major functional differences between different protein families. To compare them,I have used the structural data from the PDB database and sequences from the UniProt database. ...protein structure on the example of small GTPases. The first results are not ...
839 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
840 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.
841 4dlp - High Throughput Virtual Screening to Identify Novel natural product Inhibitors for MethionyltRNA-Synthetase of Brucella melitensis 2017 M Kumari, S Chandra, N Tiwari, N Subbarao - Bioinformation, 2017 - ncbi.nlm.nih.gov ... IV, and Methionine analogus dataset respectively. The crystal structure of MetRsBm(4DLP) was obtained from protein data bank (http://www.rcsb.org/pdb/explore.do?structureId=4DLP). The protein was prepared by removing ...
842 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
843 4dlp - Functional effect of alterations to E. coli methionyl-trna synthetase -linker length 2015 Y Xia - 2015 - search.proquest.com ... Table 2. Crystal structure of MetRS with different ligands. Organism Ligand PDB id Reference E. coli No ligand 1QQT 2. E. coli Methionine 1F4L 40. E. coli Methionine phosphonate 1P7P 41. ... A. aeolicus tRNAMet 2CSX 11. B. melitensis Selenomethionine 4DLP 42. ...
844 4dq8 - Green synthesis, antitubercular evaluation, and molecular docking studies of ethyl 3, 5-dicyano-6-oxo-2, 4-diarylpiperidine-3-carboxylate derivatives 2020 T Sekhar, P Thriveni, K Ramesh, PG Prasad- Medicinal Chemistry, 2020 - Springer Full size image. Fig. 4 figure4. a 3D structure view of molecular docking of compound 4c (green sticks) with Mycobacterium AckA protein (gray lines) The PDB file of the target protein downloaded from RCSB PDB (www.rcsb.org), AckA (PDBID: 4DQ8 )
845 4dq8 3r9p, 3p4i, 4ijn Investigation of pyrophosphate versus ATP substrate selection in the Entamoeba histolytica acetate kinase 2017 T Dang, C Ingram-Smith- Scientific Reports, 2017 - ncbi.nlm.nih.gov ... ID 3P4I; Mycobacterium paratuberculosis, PDB ID 3R9P; Mycobacterium marinum PDB ID 4DQ8 . ... ACK structures were downloaded from Protein Data Bank ( PDB ): 4H0O (Entamoeba ... Structure superposition and modeling were performed using Accelrys Discovery Studio 3.5 ...
846 4dut - Structural and Functional Characterization of Acinetobacter baumannii Nucleoside Diphosphate Kinase 2015 Progress in Biochemistry and Biophysics, 2015, 42(3): 260-267 ... 82.12. 2.4 Structure determination and refinement. Initially,wild type structurewas determined by molecular replacement (MR) method using Burkholderiathailandensis NDK (PDB code 4DUT) as starting model. After ...
847 4dxl - Oxadiazole and phenol derivatives as antibacterial and/or herbicidal agents 2018 TJ Hagen, M Thompson, JR Troxell- US Patent App. 15, 2018 - Google Patents To date, there are 17 crystal structures of six different species of IspE deposited in the PDB with 17 different ligands FIG. 11 . X-Ray Crystal Structure of Mycobacterium abscessus IspE with ATP (red) and CMP (blue) Bound to Active Site; PDBID 4DXL . FIG. 12
848 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 ...
849 4dz4 - Elucidao estrutural da especificidade por substratos de enzimas da biossntese de aminoglicosdeos e marginolactonas 2020 TP Cardoso - 2020 - repositorio.unesp.br Marginolactone. Structure . Page 9. Lista de Ilustraes AERUGINOSA: GPUA- Q9I6K2; S. CLAVULIGERUS: PAH - P0DJQ3; B. THAILANDENSIS: BUR- Q2T3W4 [ 4DZ4 CDIGO DO PDB ]; D.RADIODURANS: DR_AGM- Q9RZ04; B. CALDOVELOX
850 4dz4 - Clonamiento y anlisis funcional de la agmatinasa de ratn 2016 R Carrera, N Natalia - 2016 - repositorio.udec.cl Page 1. Universidad de Concepcin Direccin de Postgrado Facultad de Ciencias Biolgicas - Programa de Magster en Bioqumica y Bioinformtica Clonamiento y anlisis funcional de la agmatinasa de ratn. Tesis para optar PDB ID: 4DZ4. X -ray crystal structure of a hypothetical Agmatinase from Burkholderia thailandensis. ...
851 4dz4 -