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 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 ...
2 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
3 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
4 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- ...
5 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 ...
6 4ffc - Polyamines in fungi 2016 J Ruiz-Herrera - 2016 - 5.63.15.51 ... come from such different sources and have in common only their chemical similarities: Polyaminealiphatic molecules (see their structures in Figure ... Figure 3.15 structure of a 4-aminobutyrate aminotransferase (GabT) from Mycobacterium abscessus, 4FFC (Baugh, l., Phan, i., Begley, D.W., Clifton, m.c., Armour ...
7 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). ...
8 4f4h - Caracterizao de enzima nad sintetase (NADE2) de herbaspirillum seropedicae 2016 ARS Santos - 2016 - acervodigital.ufpr.br ... Outras NAD sintetases de procariotos com domínio glutaminase como a de Cytophaga hutchinsonii (número PDB 3ILV) e Burkholderia thailandensis (número PDB 4F4H), possuem estruturas cristalinas determinadas e depositadas no banco de dados PDB. ...
9 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) ...
10 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 ...
11 4kna - Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket 2017 JH Bertram, KM Mulliner, K Shi - Applied and , 2017 - Am Soc Microbiol ... The closest homologous structures currently available are those reported under PDB accession no. 4KNA (N-succinylglutamate 5-semialdehyde dehydrogenase from Burkholderia thailandensis) and 3JU8, with amino acid sequence identities of 63% and 62%, respectively. ...
12 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. ...
13 4kna - Characterization of five fatty aldehyde dehydrogenase enzymes from Marinobacter and Acinetobacter: structural insights into the aldehyde binding pocket 2017 JH Bertram, KM Mulliner, K Shi - Applied and , 2017 - Am Soc Microbiol ... Furthermore, we 70 selected one enzyme for structural studies, and here report the ... The closest homologous structures currently available are 4KNA (N-succinylglutamate 5-semialdehyde dehydrogenase from Burkholderia thailandensis) and 3JU8, with amino acid sequence identity of 63% and 62% respectively. ...
14 4w65 - Functional analysis of a novel -(1, 3)-glucanase from Corallococcus sp. EGB containing a fascin-like module 2017 J Zhou, Z Li, J Wu, L Li, D Li, X Ye, X Luo - Applied and , 2017 - Am Soc Microbiol ... The GH16 domain sequence of LamC was aligned with the following proteins: β-(1,3)-glucanase A1 (GlcA) from B. circulans (accession no. P23903), ... and the glycoside hydrolase family protein from Mycobacterium fortuitum (PDB no. 4W65) ...
15 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
16 4wxt - Reposicionamento de frmacos para malriaum mtodo que identifica alvos no domnio das doenas negligenciadas 2015 E Barante - 2015 - arca.icict.fiocruz.br ... the know-how of many technological areas, with focus on information, computing, and, particularlyon the construction and use of existing Internet databases such as MEDLINE, PubMed and PDB. ...The problems appear by the lack of textual structure or appropriate markup tags. ...
17 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 ...
18 4xfj 4oh7 FreeSASA: An open source C library for solvent accessible surface area calculation 2016 S Mitternacht - arXiv preprint arXiv:1601.06764, 2016 - arxiv.org ... 88 PDB files were selected randomly from a set of size intervals ... PISCES specifies a specific chainin each structure, but in the following all chains were used, which resulted in the ... 4c1a, 4cj0, 4g6t,4g7x, 4gmu, 4h7u, 4kv7, 4la2, 4lix, 4n13, 4oh7, 4oxx, 4p0t, 4pj2, 4qas, 4xfj, 7odc. ...
19 3p32 - Prediction of Flavin Mononucleotide (FMN) Binding Sites in Proteins Using the 3D Search Motif Method and Double-Centroid Reduced Representation of Protein 3D Structures 2015 A Banerjee, VM Reyes - arXiv preprint arXiv:1602.08119, 2015 - arxiv.org ... Since this work utilizes the benefits of using a DCRR structure as opposed to a AAR structureas discussed above one of the very important steps is to convert the structures into DCRR onesfrom the default AAR structure given in PDB. There can be two ways of doing this. ...
20 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
21 4fky - The antigenic evolution of human influenza A haemagglutinin 2013 WD Lees - 2013 - bbktheses.da.ulcc.ac.uk ... indicative results much more quickly than laboratory assays; - The use of large bodies ofsequence data in combination with structural information in ... 1.1 Influenza Structure InfluenzaA is an enveloped negative-sense RNA virus (Figure 1.1). It has two surface ...
22 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 ...
23 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 ...
24 4fur - Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences 2016 FD Richard, R Alves, AV Kajava - Bioinformatics, 2016 - Oxford Univ Press ... Examples of proteins where TRs found in sequence either correspond to (A) presence (PDBcode 3VN3 (Kondo et al., 2011)) or (B) absence (4FUR) of TRs ... both in sequence and in structure(TR-SS) and 'false' TRs only found in sequence but not in the structure (TR-SNS ...
25 6w7x - Biochemical Characterization and Structural Analysis of N-acetylornithine Transaminase from Synechocystis sp. PCC6803 2021 F BAI, Z LI, X WANG, Z HU, L BAO- Biotechnology, 2021 - biotech.aiijournal.com PLP PLP slr1022, 2E54, 6W7X , 2EH6 and SWISS- MODEL N- PDB ID 2E54 A: Cartoon structure of Slr1022
26 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 ...
27 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. ...
28 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 ...
29 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 ...
30 4ffc - Polyamines in Fungi: Their Distribution, Metabolism, and Role in Cell Differentiation and Morphogenesis 2015 L Valds-Santiago, J Ruiz-Herrera - 2015 - books.google.com ... of Polyamines.....5 2.1 Introduction.....5 2.2 Chemical Structure and Physicochemical ... of theInteractions of Polyamines with Cell Macromolecules and Structures..... ...
31 4ohc - Orotato fosforribosiltransferasa. Pasado, presente y futuro en el estudio estructural de las protenas. 2020 L Gonzlez-Segura, EI Carrizosa-Carbajal - bq.facmed.unam.mx Past, present and future in the structural study of proteins Key words: Phosphoribosyltransferase; three- dimensional structure ; conformational change; inhibition; pyrimidines synthesis str (PDBs 3M3H y 4RV4), de Burkholderia cenocepacia ( PDB 4OHC ), de Corynebacterium
32 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). ...
33 4ed9 - Overexpression and Purification of the Protein BaiK for Structural Characterization by X-Ray Crystallography 2020 S Khuu - 2020 - broncoscholar.library.cpp.edu Initially , BaiK was overexpressed to produce large quantity of protein for use in structural and structure being very similar to histidine while also being added at a high concentration. 11 formation of more ordered crystal structures . The effective concentration of the protein
34 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 ...
35 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 ...
36 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 .... ...
37 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 ...
38 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
39 4emd 4dxl, 4ed4 Evaluation of IspE for inhibitor design in the non-mevalonate pathway 2018 KB Hoerchler - 2018 - commons.lib.niu.edu crystal structures were obtained ( PDB : 1UEK, 1OJ4).38,39 IspE possesses structural features Figure 1-5. Crystal Structures of MaIspE The left structure ( PDB : 4EMD ) co-crystallized with CMP and a sulfate ion while the right ( PDB : 4ED4) co-crystallized with ATP.42
40 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).
41 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). ...
42 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...
43 4wi1 - Drug targeting of one or more aminoacyl-tRNA synthetase in the malaria parasite Plasmodium 2018 Y Manickam, R Chaturvedi, P Babbar- Drug Discovery, 2018 - csmres.co.uk site of Pf-LRScyto effectively and the crystal structure for the editing domain of enzymes with this scaffold is known different inhibitor molecules: halofuginone (HF, yellow PDB ID: 4YDQ), glyburide (violet, PDB ID: 5IFU), TCMDC-124506 (orange, PDB ID: 4WI1 ) and modeled
44 4h51 - Mitochondrial selfish elements and the evolution of biological novelties 2016 L Milani, F Ghiselli, M Passamonti - Current Zoology, 2016 - cz.oxfordjournals.org ... and to better show the structure of both male and female acinus (ie, the structural unit of ... The tertiarystructure of RPHM21 and RPHF22 was predicted using I-TASSER (http://zhanglab.ccmb.med ...The best model in pdb format was used as input for the Chimera 1.8.1 software ...
45 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
46 4u7x - Mrub_3029, Mrub_2052, are predicted orthologs of b_0688, b_0394, while Mrub_0759 and Mrub_2365 are not predicted orthologs of b_1309, in Escherichia coli, 2017 MA Benstine, D Scott, R Lori - 2017 - digitalcommons.augustana.edu ... Next, the Protein Data Bank (PDB) is accessed which gives 3-D models of protein structures ourgene is found in, it helps portray how the protein is folded which helps predict function (Bernmanet al, 2003). ... Protein Database (4U7X) Crystal structure of Fructokinase from ...
47 5ids - Mrub_2052, Mrub_0628, and Mrub_2034 genes are predicted to be orthologous to b0688, b2039, and b3789 genes found in Escherichia coli, which are involved in 2017 JP Hartnett, D Scott - 2017 - digitalcommons.augustana.edu ... (Finn et al.). Protein Data Bank ( PDB ) (Berman et. al., 2000) is a curated collection of crystalized proteins.If a PDB hit is obtained for a query sequence, then 3-D structure neighbors, Page 7. 6 ... PDB protein database 5IDS Glucose-1-phosphate Thymidylyltransferase ...
48 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 ...
49 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 ...
50 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
51 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. ...
52 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. ...
53 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), ...
54 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 ...
55 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) ...
56 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 ...
57 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 ...
58 4ohc - Investigations into patterns of interactions involving sequentially neighboring amino acids in functional proteins 2016 M Sule - 2016 - dspace.ncl.res.in Figure 6. The alpha helix in PDB : 3KB9 with the side chain hydrogen bonding pattern between While most motifs comprise primarily of regular secondary structures such as -helices or -sheets, the regions connecting these structural elements are irregular structure elements
59 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. ...
60 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. ...
61 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 ...
62 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 ...
63 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 ...
64 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). ...
65 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. ...
66 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. ...
67 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 ...
68 4ed9 - Function and X-Ray crystal structure of Escherichia coli YfdE 2013 EA Mullins, KL Sullivan, TJ Kappock - PloS one, 2013 - dx.plos.org ... the same orientation as Figure 4B. PDB entries are 4hl6 (white), 4ed9 (dark blue), 1p5h (green) [69], 1pt7 (cyan) [24], 3ubm (orange) [25], 1*k7 (yellow) [70], 1*74 (magenta) [71], and 2g04 (pink) [72]. (B) ML phylogram of the ...
69 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. ...
70 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. ...
71 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
72 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 ...
73 4ex5 - Structural Basis for the Site-Specific Incorporation of Lysine Derivatives into Proteins 2014 V Flgel, M Vrabel, S Schneider - PloS one, 2014 - dx.plos.org ... A structure of the LysRS from Bacillus stearothermophilus (PDB code 3A74), Bulkholderia thailandensis (PDB code 4EX5 [38]) and Escherichia coli (PDB ... Atomic coordinates were submitted to the Protein Data Bank (http://www.ebi.ac.uk/pdbe/) with the PDB codes: 4CH6 ...
74 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]. ...
75 4o2d - Biochemical and Structural Characterization of Mycobacterial Aspartyl-tRNA Synthetase AspS, a Promising TB Drug Target 2014 SS Gurcha, V Usha, JAG Cox, K Fütterer, KA Abrahams… - PloS one, 2014 - dx.plos.org ... The corresponding loop in E. coli AspRS is 11 amino acid residues shorter (Figure 7). Anapo-structure of Ms-AspS has recently been deposited in the PDB (entry 4O2D), in which thisloop assumes a very different conformation, forming a 2-turn α-helix and folding back ...
76 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 ...
77 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 ...
78 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 ...
79 4i1v - Tethering of Epidermal Growth Factor (EGF) to Beta Tricalcium Phosphate (βTCP) via Fusion to a High Affinity, Multimeric βTCP-Binding Peptide: Effects on … 2015 LM Alvarez, JJ Rivera, L Stockdale, S Saini, RT Lee… - PloS one, 2015 - dx.plos.org ... The TT motif has been implicated in the interactions of dephospho-CoA kinases with the diphosphate group of adenosine di-phosphate (ADP) through hydrogen bonding mechanisms (PDB ID#s: 1JJV, 4I1V; [83]), suggesting a potential role for the TT motif in our binding peptide for interaction with calcium phosphate ...
80 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
81 6dj8 - COMPARISON OF STRUCTURAL PROTEIN OF SILKWORM DENSOVIRUS BMDNV-1 WITH PROTEINS OF VIRUSES OF BACTERIA AND ARCHAEA TO STUDY THE POSSIBILITY OF FALSE POSITIVE ANSWERS IN THE ELISA - TESTING OF CATERPILLARS 2020 Antonovich ZA, Nazipova NN, ..., Scientific Journal of KubSAU , 2020 - ej.kubagro.ru PDB . . , SMTL ID : 6dj8 .1 ( Structure of DNA polymerase III subunit beta from Borrelia burgdorferi)
82 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 ...
83 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. ...
84 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
85 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. ...
86 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. ...
87 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. ...
88 5ihp - Structural studies of the DNA partitioning protein IncC from the plasmid RK2 2018 MFU Rehman - 2018 - etheses.bham.ac.uk Page 1. Structural Studies of the DNA Partitioning Protein IncC from the Plasmid RK2 By 251 6.15.2 Crosslink- structure mapping using IncC2 models 23 1.16 Structures of DNA/centromere binding proteins (CBP) 25 1.17 C- and N- terminals of KorB protein
89 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 ...
90 4dz4 - Characterising two genomic islands involved in metabolism in Neisseria meningitidis 2017 AJ Chu - 2017 - etheses.whiterose.ac.uk Figure 3.1-1 Simplified chemical structures of polyamines ----- 47 characterisation of the meningococcal pili structure demonstrates the organism's 135, X, Y, Z and 29E were duly classified based on structural variations in capsular
91 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
92 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). ...
93 4odj - Redox regulation of Plasmodium falciparum methionine adenosyltransferase and Mycetinis scorodonius DyP-type peroxidase 1 2016 J Pretzel - 2016 - geb.uni-giessen.de ... Since the crystal structure of PfalMAT is not yet available, we constructed a homology model based on the crystal structures of MAT from different organisms, the alpha subunit of human MAT isoform 2 (hMAT2A) (PDB ID 2p02) and C. hominis MAT (PDB ID 4odj) ...
94 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. ...
95 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. ...
96 4ncx - Parallelization of large-scale Drug-Protein binding experiments 2017 A Makris, D Michail, I Varlamis- & Simulation (HPCS, 2017 - ieeexplore.ieee.org ... pair of proteins 4M10 (the structure of Murine Cyclooxygenase-2 Complex with Isoxicam) and 3KQZ (the structure of a ... random motifs malaria motifs 4fm5 42 6cox 27 3kwb 7 4ncx 23 1cjb 25 1nnu 10 1d3z 3 1cmx ... correspond to protein chains, only the distinct PDB IDs were kept. ...
97 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 ...
98 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 ...
99 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. ...
100 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. ...
101 5woq - In-Silico Structural & Molecular Characterization Of Clgr From Mycobacterium Tuberculosis 2018 YN Joshi, RD Salunkhe - ijiset.com was obtained through SWISS MODEL server using resolution 1.8 A structure of ClgR from Mycobacterium smegmatis ( PDB Id: 5woq .2.A K, Bordoli L, Kopp J, Schwede T. The SWISSMODEL Workspace: A web-based environment for protein structure homology modelling
102 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. ...
103 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]). ...
104 4lfy - Dihydroorotase from Bacillus anthracis and Staphylococcus aureus 2016 AJ Rice - 2016 - indigo.uic.edu 2.1 Introduction Class II DHOase from E. coli has been studied at length, producing many apo and complex crystal structures (Table I). The structure revealed DHOase is a homodimer zinc metalloenzyme Organism PDB Ligand Modification Burkholderia cenocepacia 4LFY Apo
105 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). ...
106 4j07 - The eradication of leprosy: molecular modeling techniques for novel drug discovery 2013 S Anusuya, J Natarajan - Expert opinion on drug discovery, 2013 - informahealthcare.com ... M. leprae (Table 1) were elucidated using X-ray diffraction methods and were deposited in ProteinData Bank (PDB). ... In case of the structure of riboflavin synthase (PDB ID: 4JO7), the resolution is 1.95 ? which ... Table 2. Results of Ramachandran plot analysis for 1BVS and 4J07. ...
107 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 ...
108 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- ...
109 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
110 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
111 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 ...
112 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 ...
113 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 ...
114 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 ...
115 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. ...
116 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
117 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 ...
118 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.
119 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. ...
120 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 ...
121 5dwn - Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex 2017 EJ Loveridge, C Jones, MJ Bull, SC Moody - Journal of , 2017 - Am Soc Microbiol ... protein [37], including conservation of the bleomycin-binding regions), phosphinothricinN-acetyltransferase (36% identical to phosphinothricin N-acetyltransferase from Brucella ovis[GenBank accession number WP_006155257; PDB accession number 5DWN], with significant ...
122 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.
123 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. ...
124 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) ...
125 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.
126 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. ...
127 4odj - Characterization and redox regulation of Plasmodium falciparum methionine adenosyltransferase 2016 J Pretzel, M Gehr, M Eisenkolb, L Wang - Journal of , 2016 - Jpn Biochemical Soc ... The structure of PfalMAT was modelled according to the crystal structures of MAT2A fromHomo sapiens (PDB no. 2p02) and Cryptosporidium hominis (PDB no. 4odj) using theSWISS-MODEL automated comparative protein-modelling server (36). ...
128 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 ...
129 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 ...
130 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+ ...
131 4f2n - Imidazole-containing phthalazine derivatives inhibit Fe-SOD performance in Leishmania species and are active in vitro against visceral and mucosal leishmaniasis 2015 M Sánchez-Moreno, F Gómez-Contreras… - Parasitology, 2015 - Cambridge Univ Press .. The Fe-SOD enzymes structure were obtained from the Brookhaven protein data bank (entry 2gpc for Trypanosoma cruzi and entry 4F2N for Leishmania, corresponding to L. major, as it is the only published structure for a Leishmania species) and their energies were minimized ...
132 4f4e - Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6 2015 A Bujacz, M Rutkiewicz-Krotewicz… - Biological …, 2015 - journals.iucr.org ... PDB references: PsyArAT, 4rkc complex with aspartate, 4rkd [Cited in] [Download citation ... Crystalstructure and enzymatic properties of a broad substrate-specificity psychrophilic ... Here, geneisolation, protein expression, purification, enzymatic properties and structural studies are ...
133 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 ...
134 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 ...
135 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 ...
136 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 ...
137 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);...
138 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 ...
139 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) ...
140 5enu - An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins 2017 AF Harper, JB Leuthaeuser, PC Babbitt - PLOS Computational , 2017 - journals.plos.org ... the PFAM family, and structural modelling to create active sites; ultimately structural comparisonsare ...Notably, the invariant Gly, Ser, and Asp of the G(V/I)SxD motif are all in the 5ENU active site, along with the conserved Leu. These distinctive features suggest that, indeed, these two subgroups are functionally distinct.. ...
141 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. ...
142 4lgv - Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies 2016 M Fuentealba, R Muoz, P Maturana, A Krapp - PloS one, 2016 - journals.plos.org ... Four additional G6PDH sequences were included: those from Mycobacterium avium(Actinobacteria), whose structure is known (PDB ID 4LGV), from Borreliaburgdorferi (Spirochaetes),Synechocisits (Cyanobacteria) and Chlamydophila pneumoniae (Chlamydiae). ...
143 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 ...
144 4h51 4w5k, 3meb Structural Insights into a Novel Class of Aspartate Aminotransferase from Corynebacterium glutamicum 2016 HF Son, KJ Kim - PloS one, 2016 - journals.plos.org ... A) RMSD of reported AspAT structures were analyzed. PDB code 1SPA; Escherichia coli, 7AAT; Gallus gallus (cytosolic), 2CST; Gallus gallus (mitochondrial), 3PD6; Mus musculus, 4W5K; Trypanosoma brucei, 1AJR; Sus scrofa, 3MEB; Gaiardia lamblia, 1YAA; Saccharomyces cerevisiae, 4H51; Leishmania major, 3K7Y; Plasmodium falciparum, ...
145 4w91 - Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU 2016 B Blauenburg, A Mielcarek, F Altegoer, CD Fage - PLoS , 2016 - journals.plos.org ... As no structure of B. subtilis SufS was available at the start of our study, we sought to fill this gap.BsSufS was thus crystallized and its structure was determined to 1.7 resolution by molecularreplacement using the B. suis homolog (PDB ID 4W91) [41] as a search ...
146 4nps 4wgj Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin 2016 FV Stanger, A Harms, C Dehio, T Schirmer - PloS one, 2016 - journals.plos.org ... Depending on the conservation of crucial active site residues, the FIC fold serves as structuralscaffold for various enzymatic activities, mostly ...The lack of electron density of the flap of the E28G mutant has already been observed in several other FIC domain protein structures (e.g. Bep1 from Bartonella clarridgeiae, PBD: 4NPS or NmFicE102R from Neisseria meningitidis, PDB: 5CGL). ...
147 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 ...
148 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 ). ...
149 4ijn - Sugar analog synthesis by in vitro biocatalytic cascade: A comparison of alternative enzyme complements for dihydroxyacetone phosphate production as a 2017 CJ Hartley, NG French, JA Scoble, CC Williams- PloS one, 2017 - journals.plos.org of pH 7.09.0 and between 2537C. Most of the selected enzymes had known crystal structures (those with ATP-recycling enzymes, two acetate kinases (AceK) from Mycobacterium smegmatis and Methanosarcina thermophila (AceK Ms ; WI_011727188; PDB 4IJN and AceK
150 4jpd - SAXS and stability studies of iron-induced oligomers of bacterial frataxin CyaY 2017 M Fekry, W Alshokry, P Grela, M Tchrzewski- PloS one, 2017 - journals.plos.org ... The crystal structure of the CyaY monomer ( PDB entry 1EW4) was used for building a model, which was assumed to be a ... The ratio between the emission intensities at 350 nm and 330 nm (F350/F330) was used to track the structural changes with increasing temperature. ...
151 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 ...
152 5dvw - Computational Drug Design against Ebola Virus Targeting Viral Matrix Protein VP30 2019 A Venkatesan, L Ravichandran- Borneo Journal of, 2019 - journal.umpalangkaraya.ac.id Protein structure preparation The protein crystal structure of Ebola VP30 protein ( PDB code: 5DVW ) with the resolution of 1.75 was retrieved from RCSB Protein Data Bank ( PDB ), a repository providing crystal structures of biotic macromolecules (Berman et al., 2000)
153 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 ...
154 4qtp - Mycobacterium avium subsp. paratuberculosis 감염 초기 개체 검출을 위한항원 탐색 및 특성 분석 2015 박홍태, 박현의, 신민경, 조용일, 유한상 - Korean J Vet Res, 2015 - kjvr.org ... MAP의 MAP0380 유전자가 coding하고 있는 anti-sigma factor antagonist protein(PDB ID: 4qtp,TM-score ... 1. Three-dimensional structure prediction using I-TASSER server. ... 백질은 MAP1204의p60 domain으로 나타났는데(PDB ID: 3i86, TM-score: 0.547), sequence identity가 100 ...
155 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 ...
156 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 ...
157 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 ...
158 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
159 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 ...
160 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 ...
161 4lc3 - Structural and functional characterization of a unique hypothetical protein (WP_003901628. 1) of Mycobacterium tuberculosis: a computational approach 2017 R Uddin, S Rafi- Medicinal Chemistry Research, 2017 - Springer ... 2011). Table 8 RMSD of top Z-ranked ProBis ligands after docking with modeled structure . S.No. PDB ID. 1 st ranked RMSD (). Lowest RMSD (). 1. 1O69. 4.93. 3.45. 2. 1MDO. 3.02. 2.89. 3. 2C81. 6.43. 3.9. 4. ... 8. 3UWC. 3.37. 3.36. 9. 4K2M. 9.68. 2.5. 10. 4LC3 . 8.24. 3.91. 11. 1B9H ...
162 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 ...
163 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 ...
164 4whx 3u0g First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for l-amino acids and R-amines 2016 KM Boyko, TN Stekhanova, AY Nikolaeva - Extremophiles, 2016 - Springer ... Secondary structure elements were assigned by DSSP (Touw et al. ... In the previously describedstructures of holo BCATs (PDB codes: 3U0G, 1I1K, 1WRV), the interdomain loop was found tobe ... 7) as well as in complexes of other BCATs (for example: 2EIY, 1IYE, 4WHX and 1I1L ...
165 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 ...
166 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 ...
167 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
168 4ed9 - C7orf10 encodes succinate-hydroxymethylglutarate CoA-transferase, the enzyme that converts glutarate to glutaryl-CoA 2014 S Marlaire, E Van Schaftingen… - Journal of inherited …, 2014 - Springer ... Electrophoresis was performed with ≈50 μg protein for the Coomassie Blue stained gel and ≈5 μg (soluble proteins) or ≈1 ... The closest homologue of human C7orf10 for which a structure is available (4ED9) shares more than 40 % se- quence identity with the mammalian ...
169 4fkx - Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization 2017 AK Mishra, N Singh, P Agnihotri, S Mishra - Journal of Computer- , 2017 - Springer ... novel LaNDK inhibitors, the crystal structure of Leishmania major NDKb in complex with ADP(PDB ID: 3NGU ... three fold virtual screening uti- lizing Surflex-dock, GeomX and Flex-X, as ourstructure lacks the ... TbNDK (4FKX) 32,672 14,027 20,443 3566 32.7 6.6 Hexamer Dimer ...
170 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 ...
171 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. ...
172 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. ...
173 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 ...
174 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 ...
175 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 (
176 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 ...
177 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 ...
178 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. ...
179 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 ...
180 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 ...
181 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. ...
182 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]. ...
183 4fkx - Protein Secondary Structure Detection Using Dihedral Angle Parameters Evaluation 2014 M Diez, V Petuya, I Mart?nez, A Hern?ndez - The 11th IFToMM International Symposium on Science of Mechanisms and Machines Mechanisms and Machine Science , 2014 - Springer ... To check the results obtained with the procedure, they have been compared with each proteins' structural data, available on the Protein Data Bank (PDB) and experimentally obtained. ... 1zac. 96.6. 1k9p. 96.62. 3cln. 97.2. 1k20. 93.48. 2peq. 100. 4fkx. 82.35. 3sza. 86.6. ...
184 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 ...
185 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.
186 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
187 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). ...
188 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). ...
189 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. ...
190 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 ...
191 4gl8 - Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter 2017 AM Groshong, A Dey, I Bezsonova, MJ Caimano- mBio, 2017 - Am Soc Microbiol Structural features distinguish BbOppA4 from Gram-negative and Gram-positive OBPs.We took advantage of the crystal structure of BbOppA4 ( PDB ID: 4GL8 ) (39) to determine if B. burgdorferi OBPs possess structural elements compatible with promiscuous peptide binding, the
192 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. ...
193 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 ...
194 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). ...
195 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...
196 5eo6 4wsh, 4exq Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product 2017 HA Dailey, TA Dailey, S Gerdes, D Jahn… - Microbiology and …, 2017 - Am Soc Microbiol ...the structures of CgdC from yeast (PDB accession number 1TLB), human (accession number 2AEX), Leishmania major (accession number 3DWR), Leishmania donovani (accession number 3EJO), Leishmania naiffi (accession number 3E8J), and Acinetobacter baumannii (accession number 5EO6) have been solved, with all of them revealing an unprecedented fold for the monomer of large seven-stranded antiparallel β-sheets covered on both sides by α-helices..
197 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 ...
198 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 ...
199 5i3e - Benzoyloxy-ethyl-carbamic acid: A novel anticancerous secondary metabolite produced by Streptomyces globosus VITLGK011 2017 L Ravi, K Krishnan - 2017 - nopr.niscair.res.in A total of 11 drug target proteins were chosen and the 3D structure was downloaded from PDB website (www.rcsb.org) with the following PDB -ID: 5JSN, 5FMJ, 5J9Y, 2YJA, 3G73, 5FWL, 5I3E , 5JSB, 3S4E, 5HA9, and 5HHD. Downloaded protein structures were prepared for
200 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 ...
201 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. ...
202 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 ...
203 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 ...
204 4lgv - The structure of a Trypanosoma cruzi glucose6phosphate dehydrogenase reveals differences from the mammalian enzyme 2016 GF Mercaldi, A Dawson, WN Hunter - FEBS letters, 2016 - Wiley Online Library ... In M. avium and L. mesenteroides G6PDHs (PDB codes 4LGV and 1DPG respectively), thiscysteine is replaced by a valine and an alanine ... The cavity in the T. cruzi enzyme offersopportunities for a structure-based approach to develop novel G6PDH inhibitors. ...
205 5idw - Structure and characterization of a NAD (P) Hdependent carbonyl reductase from Pseudomonas aeruginosa PAO1 2017 S Li, X Teng, L Su, G Mao, Y Xu, T Li, R Liu - FEBS , 2017 - Wiley Online Library ... monomer contains a large central -sheet of seven -strands that is flanked by three -helices on one side and four -helices on the other, forming a sandwich structure (Fig. ... The closest homologue is the Burkholderia vietnamiensis oxidoreductase ( PDB ID: 5IDW ; Z score 27.2 ...
206 4weo - Rational design of Meso2, 3butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations 2017 Z Pu, F Ji, J Wang, Y Zhang, W Sun, Y Bao- Febs Letters, 2017 - Wiley Online Library Sequence and structure alignment of the four BDHs. (A) Structure superposition of the BDHs in Protein Data Bank ( PDB code 1GEG: cyan; 3A28: green; 3WYE: yellow; 4WEO : red). (B) Sequence alignment between the four BDHs
207 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). ...
208 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 ...
209 4xgi - Discovery of a Potentially New Subfamily of ELFV Dehydrogenases Effective for lArginine Deamination by Enzyme Mining 2017 W Wu, Y Zhang, J Huang, Y Wu, D Liu- Biotechnology, 2017 - Wiley Online Library Active site of glutamate dehydrogenase ( PDB 4XGI ) (A), phenylalanine dehydrogenase ( PDB 1BW9) (B), valine dehydrogenase ( PDB 1LEH) (C Phenylalanine was inserted into the active site of valine dehydrogenase (C) by structure alignment of 1BW9 and
210 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: ...
211 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 ...
212 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 ...
213 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 ...
214 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, ...
215 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....
216 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. ...
217 4fi5 - Prediction of B Cell Epitopes Among Hantavirus Strains Causing Hemorragic Fever With Renal Syndrome 2016 S Kalaiselvan, S Sankar, M Ramamurthy - Journal of Cellular , 2016 - Wiley Online Library ... The 3-D predicted tertiary structure of protein for the Hantaan genotype. ... Our consensus Hantaanvirus nucleoprotein-coding aa submission had 93% (Z-score: 2.19) sequence identity withN-terminal domain of Hantaan virus strain 76118 nucleoprotein (PDB ID: 4FI5) and 79 ...
218 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. ...
219 4iuj - The influenza virus polymerase complex: an update on its structure, functions, and significance for antiviral drug design 2016 A Stevaert, L Naesens - Medicinal Research Reviews, 2016 - Wiley Online Library ... Closeup showing a superposition of the crystal structures of the PAC-PB1N interface[223] (PDB: 3CM8) on that of the FluA polymerase (light gray) and the apo form of PAC[224] (light blue; PDB: 4IUJ). ...
220 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 ...
221 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 ...
222 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 ...
223 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 ...
224 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). ...
225 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. ...
226 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. ...
227 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 ? ...
228 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: ...
229 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 ...
230 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 ...
231 4ggq - BECN2 interacts with ATG14 through a metastable coiledcoil to mediate autophagy 2017 M Su, Y Li, S Wyborny, D Neau, S Chakravarthy - Protein , 2017 - Wiley Online Library ... CCDs are unique in terms of protein folding because their tertiary structures, and often theirsecondary structure as well, are coupled to their oligomerization.34 Therefore, we assessed andcompared structural stability of the WT and seven mutant BECN2 CCD constructs using ...The atomic structures of MBP (extracted from PDB code 4GGQ), SUMO (extracted from PDB code 1L2N) and the BECN2:ATG14 CCD model were used in SASREF to build a model that was fit into the corresponding SAXS ...
232 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). ...
233 4g6c 4gnv Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress lactam antibiotic resistance 2017 G Vadlamani, KA Stubbs, J Dsir, Y Blriot - Protein , 2017 - Wiley Online Library ... iMosflm,[31] then scaled and averaged using SCALA (CCP4 package).[32] The BcNagZ:inhibitorcomplex structures were determined by molecular replacement using PHASER (from within thePHENIX package)[33] and a structure of BcNagZ (PDB ID: 4G6C) ...The position of the loop is also consistent with a previous structure of BcNagZ bound to the non-selective N-acetyl-β-glucosaminidase inhibitor 3-acetamido-4,5,6-trihydroxyazepane MM-124 (PDB ID: 4MSS)[9] and the product GlcNAc (PDB ID: 4GNV), indicating that ...
234 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. ...
235 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 ...
236 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. ...
237 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 ...
238 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 ...
239 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 ...
240 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. ...
241 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. ...
242 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 ...
243 4qgr 3njd Prediction of homoprotein and heteroprotein complexes by protein docking and templatebased modeling: A CASPCAPRI experiment 2016 MF Lensink, S Velankar - Proteins: Structure, , 2016 - Wiley Online Library ... Next article in Early View: Critical assessment of methods of protein structure prediction: Progressand new directions in round XI. ... E-mail: marc.lensink@univ-lille1.fr or Shoshana J. Wodak; VIBStructural Biology Research Center, VUB, 1050 Brussels, Belgium. ...
244 4qgr 4lc3 Templatebased modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30 2016 H Lee, M Baek, GR Lee, S Park - Proteins: Structure, , 2016 - Wiley Online Library ... The structural similarity of oligomer templates to the experimental structure of the target (releasedafter the ... T90, 0.927/2OGA, 0.927/2OGA(0.903/4LC3), 0.921/4QGR(0.915/3B8X). ... with the givendimeric state was not available in the PDB, but a dodecamer structure (PDB ID: 3RCO ...
245 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 ...
246 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 ...
247 4n0w 4oh7, 4o5m, 4o5o, 4oo0, 4m0j, 4m9a Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in doubleblind predictions during the 2017 GA Khoury, J Smadbeck, CA Kieslich - Proteins: Structure, , 2017 - Wiley Online Library ... The interface will e-mail the refined structure with a unique link to visualize the initial and refinedstructures in a Jmol environment, as well as analyze the changes in key structural features whichinclude relative GDT_TS, dDFIRE energy, and number of clashes. ...
248 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 ...
249 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 ...
250 4ege - Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases 2017 VN Are, SN Jamdar, B Ghosh, VD Goyal- Proteins: Structure,, 2017 - Wiley Online Library ... significant sequence homology with any of the known protein sequences in PDB . However, the structural superposition search using N-domain structure at Dali server ... M24 dipeptidase from Mycobacterium ulcerans ( PDB code: 4EGE ) sharing 14% sequence identity with it. ...
251 4h3e - A theoretical study on the reaction pathways of peroxynitrite formation and decay at nonheme iron centers 2014 AA Attia, R Silaghi-Dumitrescu - International Journal of Quantum Chemistry, 2014 - Wiley Online Library ... The quantum chemical calculations were performed on four chemical models. These models comprised the active sites of SOR from Pyrococcus furiosus (PDB id 1DQI) and FeSOD from Trypanosoma cruzi (PDB id 4H3E) in their ferrous and ferric forms. ...
252 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. ...
253 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 ...
254 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 ...
255 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 ...
256 4ed9 - Identifying functionally important cispeptide containing segments in proteins and their utility in molecular function annotation 2014 S Das, S Ramakumar, D Pal - FEBS Journal, 2014 - Wiley Online Library ... dots. (G), (H) and (I) depict the presence of a functionally important fragment from 1bxrA (carbamoyl phosphate synthetase) in 4ed9A (CAIB/BAIF family protein), an unknown function protein. ...
257 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 ...
258 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 ...
259 4e98 - Sensory properties of the PII signalling protein family 2015 K Forchhammer, J Lddecke - FEBS Journal, 2015 - Wiley Online Library ... In the group of P II -like proteins, the HisG proteins are special because they show P II -likestructures, which are domains of larger proteins. Name, PDB code, Organism, % Seqence Identity,% Structure Similarity, Proteins in cluster. ... CutA1, 4E98, Cryptosporidium parvum, 13, 92, ...
260 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 ...
261 4kgn - Structural and Biochemical Insights into the 2O Methylation of Pyrimidines 34 in tRNA 2017 P Pang, X Deng, Z Wang, W Xie - The FEBS Journal, 2017 - Wiley Online Library ...Figure 4. The structure and sequence comparison with orthologs from other organisms. (A) Structure overlay of the polypeptide-chain backbones in cross-eyed stereo view (represented as Cα traces) of TtTrmL (green), apo Yibk (cyan, PDB code 4KDZ), EcTrmL (magenta, PDB code 4JAK), Apo HiTrmL (yellow, PDB code 1J85), HiTrmL in complex with SAH (pink, PDB code 1MXI), Burkholderia pseudomallei TrmL in complex with SAH (gray, PDB code 4KGN). ...
262 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
263 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. ...
264 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. ...
265 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 ...
266 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 ...
267 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 ...
268 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 ...
269 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. ...
270 4f3p - Molecular and structural basis of glutathione import in Gram-positive bacteria via GshT and the cystine ABC importer TcyBC of Streptococcus mutans 2013 B Vergauwen, K Verstraete? - Molecular Microbiology, 2013 - Wiley Online Library ... binding protein HisJ of Salmonella enterica (Oh et al., 1994; Yao et al., 1994), D177 and R96 in the arginine-binding protein of Salmonella typhimurium (Stamp et al., 2011), and D180 and R98 in the glutamine-binding protein of Burkholderia pseudomallei (PDB code: 4F3P). ...
271 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. ...
272 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 ...
273 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 ...
274 4n0w - Conserved water molecules in bacterial serine hydroxymethyltransferases 2015 T Milano, ML Di Salvo, S Angelaccio… - … Design and Selection, 2015 - Oxford Univ Press ... After PDB scrutiny, 11 structures were selected on the basis of better resolution, the absenceof point ... (2003) and Mustata and Briggs (2004) who analyzed the structural role of ... MD simulationswere carried out on the dimer in the apo form of the structure 4N0W corresponding to ...
275 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. ...
276 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 ...
277 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 ...
278 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 ...
279 4ol9 - Evidence of kinetic cooperativity in dimeric ketopantoate reductase from Staphylococcus aureus. 2015 JE Sanchez, PG Gross, RW Goetze, RM Walsh… - Biochemistry, 2015 - ACS Publications ... the dimeric assembly of S. aureus KPR is conserved in the enzymes from Ralstonia eutropha, Ralstonia solanacearum, Mycobacterium tuberculosis, Enterococcus faecalis, Methylococcus capsulatus, and Bacillus subtilis (PDB entries 3HWR, 3GHY, 4OL9, 2EW2, 3I83, and 3EGO, respectively), despite low sequence identity ranging from 20−31% ...
280 4eqy - Structures of Pseudomonas aeruginosa LpxA Reveal the Basis for Its Substrate Selectivity 2015 EW Smith, XJ Zhang, C Behzadi, LD Andrews - Biochemistry, 2015 - ACS Publications ... Superimposition of all three monomers from the biologically relevant homotrimer, showing loops L1 and L2. (D) P. aeruginosa LpxA monomer superimposed onto eight ortholog LpxA monomeric structures (E. coli (PDB ID: 1LXA), B. thailandensis (PDB ID: 4EQY), ...
281 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. . ...
282 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)) ...
283 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). ...
284 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. ...
285 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%).. ...
286 4q12 4pzu Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis 2017 MM Dunsirn, JB Thoden, M Gilbert, HM Holden - Biochemistry, 2017 - ACS Publications ... and 4Q12). Whereas this protein was suggested to be a sugar N-formyltransferase, ... RelevantX-ray data collection statistics are listed in Table 1. The structure was solved via molecularreplacement with PHASER21 and using PDB entry 4PZU as a search probe. ...
287 4ex4 - Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa 2017 AC McVey, P Medarametla, X Chee, S Bartlett- Biochemistry, 2017 - ACS Publications ... G. Inactivation of these enzymes has been reported to abolish the ability of P. aeruginosa to establish infection in a mammalian model system, yet we still lack the structural information to support drug design efforts. In this work, we describe the first X-ray crystal structure of P ...
288 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
289 4lgv - Substrate Channeling in an Artificial Metabolon: A Molecular Dynamics Blueprint for an Experimental Peptide Bridge 2017 Y Liu, DP Hickey, JY Guo, E Earl, S Abdellaoui - ACS , 2017 - ACS Publications Figure 3. (A) Illustration of the proposed channeling complex using a poly(lysine) bridge as an electrostatic surface between hexokinase (HK; PDB 3VF6) and glucose-6-phosphate dehydrogenase (G6PDH; PDB 4LGV).
290 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
291 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),. ...
292 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 ...
293 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 ...
294 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). ...
295 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 ...
296 5ts2 - Umbrella Sampling and X-ray Crystallographic Analysis Unveil an Arg-Asp Gate Facilitating Inhibitor Binding Inside Phosphopantetheine Adenylyltransferase 2018 A Mondal, R Chatterjee, S Datta- The Journal of Physical, 2018 - ACS Publications In this study, we have attempted to further comprehend the structural details and mechanisms involved in AcCoA binding Material and method: MD simulations The PPATWT-AcCoA structure used for this study was obtained from RCSB- PDB ( PDB ID: 3X1J)
297 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. ...
298 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.
299 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 ...
300 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). ...
301 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 ...
302 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 ...
303 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). ...
304 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 ...
305 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 ...
306 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). ...
307 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) ...
308 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- ...
309 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 ...
310 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 ...
311 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). ...
312 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 ...
313 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 ...
314 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 ...
315 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 ...
316 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) ...
317 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 ...
318 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 ...
319 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 ...
320 4egf - A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis 2015 H Huang, MS Carter, MW Vetting - Journal of the , 2015 - ACS Publications ... 5) and (2) an experimentally verified l-xylulose reductase from M. smegmatis (MSMEG_3262;UniProt ID A0QXD6; PDB 4EGF) that shares 44 ... reaction that interconverts d-glyceraldhyde-3Pand dihydroxyacetone phosphate in glycolysis, ie, the active site structure can be ...
321 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
322 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. ...
323 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. ...
324 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. ...
325 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. ...
326 4ex5 - Dynamics of the Active Sites of Dimeric Seryl t RNA Synthetase from Methanopyrus kandleri 2015 S Dutta, N Nandi - The Journal of Physical Chemistry B, 2015 - ACS Publications ... (j) Class II AsnRS (11AS.pdb) from Escherichia coli. (k) Class II LysRS (4EX5.pdb) of speciesBurkholderia thailandesis. ... The dimeric structure of SerRS from methanogenic Methanopyruskandleri ( mk SerRS) is interesting for the following reasons. ...
327 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 ...
328 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 ...
329 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 ...
330 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 ...
331 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. ...
332 4g7f - Insights into the Giardia intestinalis enolase and human plasminogen interaction 2017 R Aguayo-Ortiz, P Meza-Cervantez, R Castillo- Molecular, 2017 - pubs.rsc.org ... P-BLAST analysis showed that T. brucei brucei ( PDB ID: 2PU1) and T. cruzi ( PDB ID: 4G7F ) exhibited the highest ... (B) Sequence alignment of the proposed HsPLG binding sites (highlighted in orange boxes) in the different organisms, (C) 3D structure superposition and ...
333 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 ...
334 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*. ...
335 4gnv - Selective trihydroxyazepane NagZ inhibitors increase sensitivity of Pseudomonas aeruginosa to beta-lactams 2013 M Mondon, S Hur, G Vadlamani, P Rodrigues? - Chemical Communications, 2013 - pubs.rsc.org ... The complex was solved by molecular replacement using a model of BcNagZ (PDB 4GNV) from which ligands and solvents were removed. ... Coordinates and structure factors for the BcNagZ?azepane complex are available in the Protein Data Bank (4MSS). ...
336 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). ...
337 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. ...
338 4ni5 - Structure-guided stereoselectivity inversion of a short-chain dehydrogenase/reductase towards halogenated acetophenones 2016 A Li, L Ye, X Yang, C Yang, J Gu, H Yu - Chemical Communications, 2016 - pubs.rsc.org ... As a powerful method to decipher a possible molecular basis for enzyme properties, structuralcomparison involving the detailed structure alignment has ... using SDRs from Drosophilamelanogaster (31% identity, PDB: 1SNY A) and Brucella suis (48% identity, PDB: 4NI5 A) as ...
339 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 ...
340 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 ...
341 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.
342 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
343 4wbs - Genetic investigation of how an ATP hydrolysis cycle is coupled to lipopolysaccharide transport 2018 BW Simpson - 2018 - rave.ohiolink.edu 36 1.3.1 Architecture of the ABC transporter family ..... 36 118 3.3.7 Crystallography data processing and structure determination ..... 118 6 Figure 1.3 MsbA undergoes structural conformational changes proposed to mediate LPS flipping This open dimer has also been observed for structures of LptB captured in the apo-state (PDB 4WBS, unpublished),
344 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.
345 4lsm - O proteoma estrutural anterior ao ltimo ancestral universal comum e suas implicaes para a evoluo das primeiras protenas 2017 B DO , I Jernimo - 2017 - rei.biblioteca.ufpb.br With the accretion of the new parts in the structure , the catalytic function emerged. Also it is suggested that the initial structural motifs RMSD: Root-Mean-Square Deviation (Raiz do Desvio Quadrtico Mdio) PDB : Protein Data-Base (Banco de Dados de Protenas)
346 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 ...
347 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
348 4g7f - Caracterizacin de la respuesta inmunolgica en el modelo murino inmunizado con la rTcENo por va subcutnea 2019 M Gutirrez Soto - 2019 - repositorioinstitucional.buap.mx Agarosa NTD Enfermedades Tropicales Desatendidas OMS Organizacin Mundial de la Salud ONU Organizacin de las Naciones Unidas OPS Organizacin Panamericana de la Salud PBS Buffer salino de fosfatos PBS-T Buffer salino de fosfatos-Tween 20 PDB Banco de
349 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...
350 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
351 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. ...
352 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 ...
353 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 ...
354 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. . ...
355 4lgv - Glicose 6-fosfato desidrogenase como alvo molecular para desenvolvimento de frmacos: estudos estruturais e identificao de inibidores 2016 GF Mercaldi - 2016 - repositorio.unicamp.br ... Comparison of this structure with the human homologous enzyme Page 10. ... contribute to improve the structural and functional knowledge about the G6PDHs, an enzyme ... A) Orientao do substrato na estrutura do complexo ternrio ( PDB 5AQ1) obtido pelo nosso grupo. ...
356 4qfh - Identificao e caracterizao de inibidores da enzima glicose-6-fosfato isomerase de Leishmania mexicana 2018 SGR Mota - 2018 - repositorio.unicamp.br A computational analysis of cavities present on LmPGI crystallographic structure suggests a potential binding site for the inhibitors PBS Phosphate Buffer Solution PDB Protein Data Bank SSGCID Seattle Structural Genomics Center for Infectious Diseases
357 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
358 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 ...
359 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 ...
360 4z9n - Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis 2018 K Keidel, F Amman, I Bibova, J Drzmisek, V Benes- RNA, 2018 - rnajournal.cshlp.org Besides its role in the stabilization of the RNA duplexes, Hfq can also actively remodel the structure of RNAs and increase or decrease the stability of BLAST search unveiled that the BP3831 protein exhibits high homology with the entry 4Z9N in the PDB protein database
361 5cy4 - Structural insights into nanoRNA degradation by human Rexo2 2019 LY Chu, S Agrawal, YP Chen, WZS Yang, HS Yuan- RNA, 2019 - rnajournal.cshlp.org 6A4E), or deposited in the protein data bank, including those from E. coli ( PDB codes: 1YTA, 2IGI), Acinetobacter baumannii ( PDB code: 5CY4 ), and Haemophilus influenzae ( PDB code 1J9A) Structural coordinates and diffraction structure factors of Rexo2-RNA, Rexo2-DNA1
362 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. ...
363 4dz6 3gp5, 3gw8 Structural and functional studies on the reactivity of CORMs with plasma proteins 2016 MFA Santos - 2016 - run.unl.pt ... 1.37 Structural representation of the vanadate(V)-RNase A adduct (PDB: 1RUV)52 ... Figure 2.7 Overall structure of HEWL bound to Ru fragments derived from ALF850 ... Figure2.8 Structural representation of RuHis15 adduct85 ...
364 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
365 6ao8 - Mutations in ArgS Arginine-tRNA Synthetase Confer Additional Antibiotic Tolerance Protection to Extended-Spectrum--Lactamase-Producing Burkholderia 2020 H Yi, J Park, KH Cho, HS Kim- Antimicrobial Agents and, 2020 - Am Soc Microbiol To investigate the ArgS function affected by the mutations, we first computationally predicted the B. thailandensis ArgS structure by using the homologous structure of Neisseria gonorrhoeae (PDB accession no. 6AO8) using Modeller
366 6xdh - A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico 2021 A Rakib, Z Nain, SA Sami, S Mahmud- Briefings in, 2021 - academic.oup.com Abstract. Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declar. ... For docking analysis, the following receptors were selected: PDB ID 6M3M for N protein, PDB ID 2GHV for the RBD of the S protein, PDB ID 6W9C for PLpro, PDB ID 6 M71 for RdRp, PDB ID 6ZSL for SARS-CoV-2 helicase (nsp13), 6WC1 for nsp9 RNA-replicase, and 6XDH for nsp15
367 6xdh - SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets 2021 AF Alsulami, SE Thomas, AR Jamasb- Briefings in, 2021 - academic.oup.com release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures , our group ... (v) Nsp15 (Uridylate specific endoribonuclease)—PDB Id: 6XDH.
368 4nbr - SCOT: Rethinking the Classification of Secondary Structure Elements 2019 T Brinkjost, C Ehrt, O Koch, P Mutzel- Bioinformatics, 2019 - academic.oup.com -bulge which leads to a kinked (highlighted in green) -helical structure in 4nbr @ pdb (chain A for SCOT and SHAFT for the structure pair 4k20@ pdb and 5cna@ pdb results from based assignment methods except for SHAFT are the most robust ones regarding structure quality
369 6q06 - Molecular diversity of coronavirus host cell entry receptors 2020 JK Millet, JA Jaimes, GR Whittaker- FEMS microbiology reviews, 2020 - academic.oup.com boxes indicate genes encoding accessory proteins (ns2, ns4a, ns4b and ns5a), while green boxes indicate structural proteins B) Representative structure of coronavirus protein in pre-fusion (S1 and S2 subunits, PDB 3JCL) and post-fusion (S2 subunit, PDB 6B3O) conformations ...MERS-CoV NTD (PDB 6Q06), which binds sialosides with a preference for α2,3-linked sialic acids,
370 6wps - Modernized uniform representation of carbohydrate molecules in the Protein Data Bank 2021 C Shao, Z Feng, JD Westbrook, E Peisach- , 2021 - academic.oup.com glycan structures (eg, SARS-CoV-2 protein-carbohydrate complex PDB ID 6WPS ) and the partnership is committed to maintaining consistency and accuracy across the PDB archive by regularly reviewing data processing procedures and carrying out structure remediation efforts
371 5ifz - SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for 2018 JM Dana, A Gutmanas, N Tyagi, G Qi- Nucleic acids, 2018 - academic.oup.com 5.3.1.34 D-erythrulose 4-phosphate isomerase Q9ZB26 99% 5ifz 5.3.1.6 Ribose-5 of the protein sequence space 40-fold, expanding the applicability of structure -based an positions from Ensembl enables a more direct cross-referencing of genomic data from PDB structures
372 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
373 5cy4 - Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA 2020 M Szewczyk, D Malik, LS Borowski- Nucleic acids, 2020 - academic.oup.com Here, we report comprehensive functional, biochemical, and structural studies to elucidate REXO2 function in human mitochondria We also demonstrate that REXO2 degrades RNA in a structure - and sequence-dependent manner. ... The model that was used for molecular replacement was oligoribonuclease from Acinetobacter baumnii (PDB ID: 5CY4, Seattle Structure Genomics Centre for Infectious Diseases), which shares 48.3% sequence identity with REXO2.
374 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.
375 6wps - CoV3D: a database of high resolution coronavirus protein structures 2021 R Gowthaman, JD Guest, R Yin- Nucleic acids, 2021 - academic.oup.com (A) Visualization of the superposed spike RBD complexes with antibody S309 ( PDB code 6WPS ) ( 20 ) and (B) A trimeric spike structure in RBD-closed conformation ( 5 ) ( PDB code 6VXX Park YJ, Tortorici MA, Wall A., McGuire AT and Veesler D. (2020) Structure , Function, and
376 6vxx - RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental 2021 SK Burley, C Bhikadiya, C Bi, S Bittrich- Nucleic acids, 2021 - academic.oup.com Biology; Nucleic Acid Enzymes; RNA and RNA-protein complexes; Structural Biology; Synthetic Biology and Bioengineering; Methods Online; Surveys and Summaries; Database; Web Server. Advance articles; Submit: Author Guidelines;
377 4o5o - A fragment-based protein interface design algorithm for symmetric assemblies 2021 J Laniado, K Meador, TO Yeates- Protein Engineering, Design, 2021 - academic.oup.com The expansive database of known protein structures provides valuable empirical frameworks for The growing focus on secondary structure associations motivates an attempt to bring by precomputing common proteinprotein fragment configurations from known structural data
378 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)
379 6bfu - Unraveling virus relationships by structure-based phylogenetic classification 2020 WM Ng, AJ Stelfox, TA Bowden- Virus Evolution, 2020 - academic.oup.com Unraveling virus relationships by structure -based phylogenetic classification. Weng M Ng. Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford. ... human coronavirus NL63 (3KBH); human coronavirus 229E (6ATK); porcine deltacoronavirus, PDCoV (6BFU). All chains not comprising S1-CTD (e.g. receptor and antibody fragments) were removed prior to structural alignment
380 5vp5 - Developing a macromolecular crystallography driven CURE 2021 KJ McLaughlin - 2021 - aca.scitation.org While these protein x-ray crystallography structures are key to allowing students to CURE that could expose and excite a next generation of potential structural scientists 3 3. KJ McLaughlin, Understanding structure : A computer-based macromolecular biochemistry lab activity, J
381 6wpt - The SARS-CoV-2 spike variant D614G favors an open conformational state 2021 RA Mansbach, S Chakraborty, K Nguyen- Science, 2021 - advances.sciencemag.org 1 Structural representation of the Spike protein. (A) The Spike complex is shown in the all-down conformation. Its S1 and S2 subunits are depicted in red and blue We display the domains highlighted in the Spike structure , shown from two different perspectives ... S309 Fab binding to up-RBD was modeled by rigid-body alignment to closed-RBD and Fab interactions from PDB structure 6WPT (21), using the backbone of residues 331 to 527 for least squares fitting.
382 6nb3 - Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM 2021 C Xu, Y Wang, C Liu, C Zhang, W Han- Science, 2021 - advances.sciencemag.org For the FP region, we first built the homology model by the Modeller tool within Chimera by using the MERS-CoV S structure (PDB: 6NB3) as template (2, 58, 59) and then used Rosetta to refine this region against the density map
383 4g6c 3laa Blind prediction of protein B-factor and flexibility 2018 D Bramer, GW Wei- The Journal of chemical physics, 2018 - aip.scitation.org MENU. SIGN IN. Sign in/Register. Enter words / phrases / DOI / ISBN / authors / keywords / etc. SEARCH; CITATION SEARCH; ADVANCED SEARCH. Search in: This Publication. search. Advanced
384 6nb4 6nb7 Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19) 2020 B Shanmugaraj, K Siriwattananon- Asian Pac J Allergy, 2020 - apjai-journal.org PDB ID 6CS2)72 and the following antibodies are shown in magenta: 80R ( PDB ID 2GHW)73, F26G1 ( PDB ID 3BGF)74, m396 ( PDB ID 2DD8)75, and S230 ( PDB ID 6NB7 (P D B ID 6NB4 ) Structure of SARS coronavirus spike receptor- binding domain complexed with receptor
385 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
386 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
387 6q05 - Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS 2020 JA Jaimes, NM Andre, JK Millet- arXiv preprint arXiv, 2020 - arxiv.org Protein Data Base: HCoV-HKU1 ( PDB # 5I08), MHV ( PDB # 3JCL), MERS-CoV ( PDB # 6Q05 ), SARS-CoV ( PDB # 5X58), FCoV-UU4 ( PDB # 6JX7), IBV-M41 ( PDB # 6CV0) and HCoV-NL63 ( PDB # 5SZS). Pairwise S structure . Additional
388 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
389 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
390 6nb7 6nb6 Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein Through Molecular Dynamics Simulation 2021 Y Li, T Wang, J Zhang, B Shao, H Gong- arXiv preprint arXiv, 2021 - arxiv.org taking the S proteins of SARS-CoV with 2 upward RBDs ( PDB ID: 6NB6) (21) and 3 upward RBDs ( PDB ID: 6NB7 ) (21) as We also conducted a time- structure based Independent Components Analysis (tICA) (34, 35) to identify slow motions with high time autocorrelation on
391 5vcu - Interpretable Neural Networks based classifiers for categorical inputs 2021 S Zamuner, PDL Rios- arXiv preprint arXiv:2102.03202, 2021 - arxiv.org cartoon representation of RAS protein (green) bounded to GDP (light blue spheres) from pdb 5vcu belonging to the most relevant predicted triplets are clustered in the structure of the Note that, to better compare to plmDCA, the same architecture and hyperparameters have
392 6axe 4ex4 The glyoxylate shunt as a target for antibacterial intervention in Pseudomonas aeruginosa 2019 AC McVey - 2019 - aspace.repository.cam.ac.uk The structure of MSG from four prokaryotic species has been resolved by X-ray crystallography: E. coli... Mycobacterium marinum (PDB entry 6AXE), and Mycobacterium leprae (PDB entry 4EX4). Also, the E. coli MSG structure has been solved by NMR
393 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
394 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
395 4k9d 4l83 Review on Computational Approaches for Identification of New Targets and Compounds for Fighting Against Filariasis 2017 M Mishra, P Srivastava- The Open Bioactive Compounds, 2017 - benthamopen.com S100a12MMDB ID: 73787 PDB ID: 2WCF [Metal Binding Protein], Glyceraldehyde 3-phosphate dehydrogenase MMDB ID: 109769 PDB ID: 4K9D etc.) in In molecular biology and structural genomics, protein structure determination has become an important area of research
396 6q05 - Evaluation of Coronavirus families & Covid-19 proteins: molecular modeling study 2020 M Monajjemi, S Shahriari- Biointerface Res. Appl, 2020 - biointerfaceresearch.com Several Proteins, receptors, S proteins including s1 and s2 such as 6LU7, 6Q05 , 4oW0, 6nur The Structure Preparation modules of MOE were used to correct PDB inconsistencies and to assign the structural knowledge of the CoV-RNA synthesis complexes was a structure of the
397 4ni5 5jy1, 4weo Phylogenetics-based identification and characterization of a superior 2, 3-butanediol dehydrogenase for Zymomonas mobilis expression 2020 V Subramanian, VV Lunin- Biotechnology, 2020 - biotechnologyforbiofuels Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. ... The initial model was built based on PDB entry 4ni5 with FFAS03 search and ProtMod modeling servers [50,51,52] using the SCWRL method.
398 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. ...
399 5t8s - Prospects of Indole derivatives as methyl transfer inhibitors: antimicrobial resistance managers 2020 S Tha, S Shakya, R Malla- BMC, 2020 - bmcpharmacoltoxicol.biomedcentral An integration of structure -based virtual screening and ligand-based virtual screening was employed to explore the antimicrobial properties of indole The X-ray diffraction structures of S-adenosyl methionine synthase, MetK from N. gonorrhoeae ( PDB id: 5T8S ) [13]; cobA from
400 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. ...
401 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]
402 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
403 5ucm - trans-Editing by aminoacyl-tRNA synthetase-like editing domains 2020 ABK Nagy, M Bakhtina- Biology of Aminoacyl, 2020 - books.google.com bound by an autonomous trans- editing factor, such as C. crescentus ProXp-ala ( PDB ID: 5VXB PheRS is also unique in its oligomeric structure it is a heterote- tramer domain ( bound in an editing active conformation will be needed to fully understand the structural basis for
404 6c5v - Gammaherpesvirus entry and fusion: A tale how two human pathogenic viruses enter their host cells 2019 BS Mhl, J Chen, R Longnecker- Adv. Virus Res, 2019 - books.google.com 323 Gammaherpesvirus entry and fusion (Waterhouse et al., 2018) based on the crystal structures of EBV gB ( PDB ID: 3FVC), gH ( 6C5V ) and gL The structural sequence alignment of EBV and KSHV gB based on the crystal structure of EBV gB (3FVC)(Backovic et al., 2009
405 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
406 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
407 5kak - Protein-protein and domain-domain interactions 2018 P Kangueane, C Nilofer - 2018 - books.google.com 1.10) structures It is important to under- stand the physical and chemical features of amino acids to understand protein folding, structure , function, and 1.4 A covalent bond is illustrated using cysteine with corresponding bond length 1.5 Structural Motifs Proteins are made of
408 5umf - Design of synthetic symmetrical proteins 2017 JRH Tameb, ARD Voet- Synthetic Biology: Volume 2, 2017 - books.google.com assembly, Ribulose-phosphate structure but since exhibits alpha 3-epimerase, C and 2 PDB : 5UMF ) and 12-fold rotational symmetry (cartoon depiction; from left to right, PDB : 4YY2, 4YXX designs will without any doubt improve our understanding of protein structure and stability
409 4hvt - Pyrococcus furiosus Prolyl Oligopeptidase: A Dynamic Supramolecular Host for Peptidase and Dirhodium Catalysis 2018 K Ellis-Guardiola, H Rui, R Beckner, P Srivastava - 2018 - chemrxiv.org both Pfu POP and the S447C mutant possess a two-domain architecture involving a peptidase domain reported homology model; M. xanthus chain A from 2BKL; R. typhi from 4HVT ; S. Scrofa from 1QFS; H. Page 17 S1). The structure of
410 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
411 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
412 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 )
413 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 ...
414 4eqy - Computer-Aided Structure-Based Drug Discovery: CXCL12, P. aeruginosa LpxA, and the Tiam1 PDZ Domain 2014 EW Smith - 2014 - scholarcommons.usf.edu ... there seems to be some noticeable variation at the C-terminal end of the third α-helix, involving dissimilar tilts compared to bacterial orthologs A. baumannii (PDB ID: 4E6U), L. interrogans (PDB ID: 3HSQ), C. jejuni (PDB ID: 3ROS), B. thailandensis (PDB ID: 4EQY),...
415 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. ...
416 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 ...
417 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);. ...
418 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 ...
419 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. ...
420 4f82 - The Crystal Structure of Peroxiredoxin Asp f3 Provides Mechanistic Insight into Oxidative Stress Resistance and Virulence of Aspergillus fumigatus 2016 F Hillmann, K Bagramyan, M Straburger - Scientific , 2016 - ncbi.nlm.nih.gov ... Asp f3's enzymatic activity on peroxides and structural similarity to the previously characterizedyeast-orthologue ... After failing to find a solution using the entire 4F82 model, flexible loops were ...PDB structure identifiers are 5J9B for WT Asp f3 and 5J9C for the C31S/C61S mutant. ...
421 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
422 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 ...
423 4zju - Battling Antibiotic Resistance by Investigation of Acinetobacter baumannii Enoyl Acyl Carrier Protein Reductase 2018 C Wong - 2018 - scholarworks.csun.edu The active site residues of abFabI in green ( PDB ID: 4ZJU , ecFabI in blue ( PDB ID: 5CFZ) and InhA in magenta ( PDB ID: 4TRM) overlay relatively Bacterial Species Year Representative PDB ID FabI homologs are similar in sequence, but the structure of their active sites may
424 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) ...
425 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. ...
426 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. ...
427 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
428 4g6c - Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM) 2015 K Xia, K Opron, GW Wei - The Journal of chemical physics, 2015 - scitation.aip.org ... More importantly, we reveal intrinsic multiscale behavior in protein structures. ... B-factor), ie, theatomic mean-square displacement, obtained in structure determination by ... depends the crystalenvironment, solvent type, data collection condition, and structural refinement procedure ...
429 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
430 6nb3 - Origen del SARS-CoV-2 desde una perspectiva Bioinformtica 2021 R Isea- Conocimiento Libre y Licenciamiento (CLIC), 2021 - convite.cenditel.gob.ve 6NB3 1359 MERS-CoV secuencias de la glicoprotena de espcula S que han sido recopiladas en la base de datos de protenas PDB Sequence analysis and structure predition of SARS-CoV-2 accesory proteins 9b and ORF14: evolutionary analysis indicates close
431 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,
432 5dvw - Napovedni modeli za identifikacijo potencialnih inhibitorjev razlinih proteinov virusa ebole 2020 V Hudi - 2020 - core.ac.uk Monte Carlo MLR Multivariatna linearna regresija mRNA Informacijska ribonukleinska kislina NP Nukleoprotein PCA Metoda glavnih komponent PDB Podatkovna knjinica Knowledge of the viral structure gives us insight into the functioning of the virus and allows us to predict
433 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
434 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 ...
435 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 ...
436 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, ...
437 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 ...
438 4v6h - X-ray crystal structure of a malonate-semialdehyde dehydrogenase from Pseudomonas sp. strain AAC 2017 M Wilding, C Scott, TS Peat, J Newman - Section F: Structural , 2017 - scripts.iucr.org ... After solving the structure, the difficulties associated with the molecular replacement from thehighly homologous sequence models became clearer, as despite their homology the structuresvary significantly. ... Similarly, PDB entry 4v6h (Seattle Structural Genomics Center ...
439 5i1f - Structure of the Bacillus anthracis dTDP-l-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA) 2017 J Baumgartner, J Lee, AS Halavaty- Section F: Structural, 2017 - scripts.iucr.org The Mg2+ ion is modeled from the RffH structure The GalU homologs are from Burkholderia vietnamiensis ( PDB entry 5i1f ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) and Sphingomonas elodea ( PDB entry 2ux8), respectively
440 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 ...
441 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 ...
442 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 ...
443 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. ...
444 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). ...
445 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 ...
446 4ixo - X-ray structures of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana 2014 T Roret, H Pgeot, J Couturier, G Mulliert - Section F: Structural , 2014 - scripts.iucr.org ... Group, PDB code, Organism, Sequence identity to AtNfs2 (%), UniProtKB accession No. Rmsd on C atoms, No. of equivalent residues to AtNfs2. ... 4eb7, 4hvk, 4ixo, Rickettsia africae, 20.7, C3PNQ7, 1.687, 218. 3a9x, Rattus norvegicus, 20.1, Q68FT9, 2.159, 263. 3a9y, 3aqz, ...
447 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 ...
448 4ege - Crystallization and preliminary X-ray diffraction analysis of Xaa-Pro dipeptidase from Xanthomonas campestris 2014 A Kumar, VN Are, B Ghosh, U Agrawal - Section F: Structural , 2014 - scripts.iucr.org ... Although the structures of XPD43 orthologues from the eubacteria Mycobacterium ulcerans, Bacillus anthracis and Thermotoga maritima (PDB entries 4ege , 3q6d and 2zsg ) have been deposited in the PDB by structural genomics consortia, none of these enzymes have been ...
449 4o2d - Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori 2017 C Songsiriritthigul, S Suebka, CJ Chen - Section F: Structural , 2017 - scripts.iucr.org ... 4a), similar to the positions of the Pro82 residue in the S. tokodaii ND- AspRS structure (Sato etal., 2007). ... Structural comparison of ND-AspRS1104 from H. pylori with those from M. smegmatis(PDB entry 4o2d; Baugh et al., 2015) and P. aeruginosa (PDB entry 4wj4 ...
450 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. ...
451 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 ...
452 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 ...
453 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 ...
454 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 ...
455 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. ...
456 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 ). ...
457 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, ...
458 4o6r - Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus 2015 AS Halavaty, RL Rich, C Chen, JC Joo… - … Section D: Biological …, 2015 - scripts.iucr.org ... DALI (Holm & Rosenstro¨ m, 2010) analysis found a putative ALDH from Burkholderia cenocepacia (PDB entry 4o6r; Seattle Structural Genomics Center for Infectious Disease, unpublished work) to be the closest structural homolog of SaBADH (Z-score of 59.6; r.m.s.d. of 1.3 A ° ; 38% sequence homology)...
459 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. ...
460 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 ...
461 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. ...
462 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 ...
463 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 ...
464 4g6z 4gri Preliminary X-ray crystallographic analysis of an engineered glutamyl-tRNA synthetase from Escherichia coli 2014 N Chongdar, S Dasgupta, AB Datta - Section F: Structural , 2014 - scripts.iucr.org ... S. & Yokoyama, S. (2010). Acta Cryst. D66, 813-820.] ). In addition, crystal structures of GluRS from Burkholderia thailandensis (PDB entry 4g6z ; Baugh et al., 2013 [Baugh, L. et al. (2013). PLoS One, 8, e53851.] ) and Borrelia ...
465 4tu1 - Structure of Toxoplasma gondii fructose-1, 6-bisphosphate aldolase 2014 LE Boucher, J Bosch - Acta Crystallographica Section F: Structural …, 2014 - scripts.iucr.org ... bound to TRAP (PDB entry 2pc4 , chain D) and TgAldolase (PDB entry 4tu1 , chains A ... highlightsthe residues important for adhesin binding in the TRAP-bound PfAldolase structure (PDB entry2pc4 ... to -helix 10 in chain A does not align with the PfAldolase structure; however, the ...
466 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%). ...
467 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. ...
468 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 ...
469 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 ...
470 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 ), ...
471 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). ...
472 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 ...
473 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 ...
474 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 ...
475 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 ...
476 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. ...
477 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
478 4xfj - HELICAL PARAMETERS OF REGULAR π-HELICES IN PROTEINS (Part 2) 2016 D. Batkhishig, B. Mijiddorj, P. Enkhbayar, 2016 - cyberleninka.ru to the DSSP program that is dedicated to identifying n-helices, which were seldom assigned by older versions of DSSP and STRIDE [7]. The secondary structure assignment methods 4XFJ A_68-74 PDB ID Chain_Po sition P (A) n Az (A)b r (A) Vc (A3) P (A) Identified Program
479 4wbs - An antibiotic binds to the ATPase that powers lipopolysaccharide transport 2016 JM May - 2016 - dash.harvard.edu This conclusion is supported by genetic, biochemical, and structural evidence, described below innermost layers of the cell envelope before turning our attention to the structure and assembly... though the C-terminus of E. coli LptB is not visible in the structures published by Sherman and collaborators, it is visible in the structure of Burkholderia phymatum LptB, crystallized with an N-terminal histidine tag in the absence of nucleotide (PDB: 4WBS)
480 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
481 4kam - Metabolic engineering of O-acetyl-L-homoserine sulfhydrylase and Met-biosynthetic pathway in Escherichia coli 2017 Y Ma - 2017 - depositonce.tu-berlin.de ... secondary structure and overall stability of investigated proteins. All these reasons highlight ... Figure 2
482 5ids - Mrub_2052, Mrub_0628, and Mrub_2034 genes are predicted to be orthologous to b0688, b2039, and b3789 genes found in Escherichia coli, which are involved in 2017 JP Hartnett, D Scott - 2017 - digitalcommons.augustana.edu (Finn et al.). Protein Data Bank ( PDB ) (Berman et. al., 2000) is a curated collection of crystalized proteins.If a PDB hit is obtained for a query sequence, then 3-D structure neighbors, Page 7. 6 PDB protein database 5IDS Glucose-1-phosphate Thymidylyltransferase
483 4u7x - Mrub_3029, Mrub_2052, are predicted orthologs of b_0688, b_0394, while Mrub_0759 and Mrub_2365 are not predicted orthologs of b_1309, in Escherichia 2017 MA Benstine, D Scott, R Lori - 2017 - digitalcommons.augustana.edu Next, the Protein Data Bank ( PDB ) is accessed which gives 3-D models of protein structures our gene is found in, it helps portray how the protein is folded which helps predict function (Bernman et al, 2003) Protein Database ( 4U7X ) Crystal structure of Fructokinase from
484 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
485 5vmk 4eqy Mechanistic characterisation and inhibitor identification of Mycobacterium tuberculosis bifunctional N-acetyltransferase/uridylyltransferase GlmU 2019 PD Craggs - 2019 - discovery.ucl.ac.uk that has contributed to the success of this pathogenic over the last thousand years. Peptidoglycan is a unique and essential structural element that provides much of the Structure of UDP-GlcN Table 7. Published GlmU structures in the Protein Data Bank ( pdb ) ....70
486 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
487 4l82 - Identification of Biological Sulfonamide Degradation 2018 B Ricken - 2018 - d-nb.info 99 4.3. Identification of enzymes responsible for SMX degradation .....103 4.4. Sulfonamides molecule structure influences biodegradability .....105 pdb|4L82| Putative Oxidoreductase Rickettsia felis
488 4whx - ω-Transaminases as Promising Biocatalysts for the Chiral Synthesis of β-Amino Acids 2018 MSO Buss - thesis The -Transaminase Engineering Database (oTAED): a navigation tool in protein sequence and structure space o Review about the protein stability engineering in silico tool FoldX ... The largest homologous family (HFam 11) includes 90% of all Fold type IV sequences and 23 annotated structures such as a branched-chain-amino-acid TA (PDB entry 4WHX)
489 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 ...
490 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
491 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
492 5i3e - Targeting Protein-Protein Interactions for Disruption of LSD1 (KDM1A) Complexes 2017 JL Schwabe - 2017 - dukespace.lib.duke.edu (b) A predicted structural model generated used to determine sites of protein-protein interactions, which can be illustrated, for example, on available crystal structures in the CoREST samples were mapped onto an available LSD1/CoREST co-crystal structure ( PDB 2IW5) as a
493 4jgb 4jga Targeting Transforming Growth Factor Beta-Activated Kinase 1 as a Therapeutic 2017 J Totzke - 2017 - dukespace.lib.duke.edu 50 3.4 Structural and functional similarities between TAK1 and related kinases ..... 50 Page 8. viii 4 Figure 2: Crystal structure TAK1 ( PDB 5V5N, left ribbon, right hydrophobicity surface) .... 11
494 4k6f - Cloning, expression and molecular modeling of the anthocyanidin reductase (FaANR) gene during strawberry fruit development. 2017 PC Mandave, AA Kuvalekar, NL Mantri, MA Islam- Fruits, 2017 - search.ebscohost.com respectively. Molecular docking study was performed on 3D structure of ANR obtained from homology modeling technique to check binding interaction of template molecule ( PDB ID: 4K6F ) with bound ligand (NADP). Ligand
495 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 ...
496 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. ...
497 5eks - In-silico three dimensional structure prediction of important Neisseria meningitidis proteins. 2021 M Ali, M Aurongzeb, Y Rashid- Pakistan Journal of, 2021 - search.ebscohost.com Chain A of 3-dehydroquinate Synthase from Acinetobacter Baumannii in complex with NAD+ with PDB id 5EKS (to be published) was selected as a template structure . The template had 98% query coverage and 56% sequence identity with the target sequence
498 6d9y 6d9n Protein secondary structure online server predictive evaluation 2019 - Chinese Journal of Bioinformatics, 2019 - search.ebscohost.com 1 SPIDER Fig.1 Main structure of SPIDER 2.1
499 4qtp - Discovery of antigens for early detection of Mycobacterium avium subsp. paratuberculosis and analysis of characteristics using bioinformatics tools. 2015 HT Park, HE Park, MK Shin, YI Cho - Korean Journal of , 2015 - search.ebscohost.com ... MAP MAP0380 coding anti-sigma factor antagonist protein(PDB ID: 4qtp,TM-score ... 1. Three-dimensional structure prediction using I-TASSER server. ... MAP1204p60 domain (PDB ID: 3i86, TM-score: 0.547), sequence identity 100 ...
500 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 ...
501 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
502 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.
503 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. ...
504 4ggq - Structural studies of the mechanism by which Bcl-2 and Beclin proteins regulate autophagy and apoptosis 2016 M Su - 2016 - search.proquest.com ... Amongst nearly 120000 structures deposited in the Protein Data Bank ( PDB ) to date, 107000 are X-ray ... of left-handed and right-handed circularly polarized light, is often used to investigate structural aspects of ... CD can be used to determine the secondary structure of proteins. ...The atomic structures of MBP (extracted from PDB code 4GGQ), SUMO (extracted from PDB code 1L2N) and Beclin 2:Atg14
505 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
506 4efz - Structural and Mechanistic Characterization of Enzymes in Persulfide Oxidation and Monolignol Biosynthesis Pathways 2018 SA Sattler - 2018 - search.proquest.com of apo-form PpPDO2 diffraction data were conducted by molecular replacement with the PDB coordinates of model 4EFZ using PHENIX Phaser (18) by molecular replacement as well, using the atomic coordinates of the unpublished structure for a
507 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
508 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). ...
509 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])
510 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
511 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. ...
512 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; ...
513 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
514 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
515 5eo6 - A Molecular, Structural, and Cellular Multiple-Level Study Aimed at Understanding the Unique Reaction Catalyzed by the Last Enzyme in the Heme-Biosynthesis 2018 AIC Luna - 2018 - search.proquest.com Overlay of the structures of a representative heme b-bound chlorite dismutase and solvent This research aimed to understand ChdC function at the molecular, structural , and cellular levels The coproheme-bound ChdC structure revealed a helical-loop that is flexible and moves
516 4h4g 3oib, 3i4e, 3e5b, 3p4t, 3p0x Structure of the Vibrio cholerae fatty acid regulator FadR 2015 W Shi - 2015 - search.proquest.com ... 3D6X, 1ZHG, 3DOY, 3DOZ, 3DP0, 3DP1, 3DP2, 3DP3, 3CF8, 3CF9, 3ED0, 3B7J, 3D04, 3AZ9,3AZ8, 3AZA, 3AZB, 4H4G, 2OKH, 2OKI ... (52, 70) and DNA-bound (PDB 1H9T and 1HW2) (69,70) structures are almost identical whereas the ligand-bound structure shows the ...
517 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 ...
518 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 ...
519 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
520 4f82 4f4a Investigating Imatinib-Resistant Mutations in Abl Kinase 2020 A Lyczek - 2020 - search.proquest.com 10 *(52& Illustration of important structural features of imatini<
521 4lgv - Multi-Scale Simulation of Electrostatic Channeling 2018 Y Liu - 2018 - search.proquest.com Figure 2-6 (a) Illustration of the proposed channeling complex using a poly(lysine) bridge as an electrostatic surface between hexokinase (HK; PDB 3VF6) and glucose-6-phosphate dehydrogenase (G6PDH; PDB 4LGV). (b) Experimental reaction scheme used to study electrostatic channeling of the charge intermediate (glucose-6-phosphate) across a cationic peptide bridge.
522 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
523 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)
524 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.
525 4iuj 4p9a Computer-Aided Drug Discovery and Protein-Ligand Docking 2015 H Li - 2015 - search.proquest.com ... In addition to PAC-PB1N structures, two apo crystal structures of PAC in the absence of PB1 have been reported recently [322]. The first is a 1.9Å resolution structure of H1N1 PAC (PDB ID: 4IUJ). The second is a 2.2Å resolution structure of H7N9 PAC (PDB ID: 4P9A)...
526 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. ...
527 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 ...
528 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
529 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
530 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. ...
531 4f0l - Structural and Biochemical Studies of C. jejuni Agmatine Deiminase, E. coli Guanine Deaminase, and S. cerevisiae Guanine Deaminase 2019 R Shek - 2019 - search.proquest.com to uric acid by xanthine oxidase. Figure 1.4. Structure of triose phosphate isomerase. PDB : 6B2W. The beta strands that make up the TIM barrel are shown in red. Page 24. 11 catalyze deamination reactions, the two families differ substantially in their structural architectures. 27
532 5i0p - STRUCTURE AND FUNCTION OF THE PALMITOYLTRANSFERASE DHHC20 AND THE ACYL COA HYDROLASE MBLAC2 2019 MIP Malgapo - 2019 - ecommons.cornell.edu crystals ..... 43 The overall structure of hDHHC20 and zfDHHC15 is similar to what was predicted for DHHC enzymes .... 44 Two zinc ions serve a structural function in the cysteine-rich domain of DHHC20 ..... 44
533 4iuj - Toward a PA-Inhibitor Complex Crystal System: Influenza Polymerase Acidic Protein Fusion Constructs and Protein Expression 2020 R Kramb - 2020 - ecommons.udayton.edu Figure 5 b (right) apo-PA crystal packing. PA ( PDB ID: 4IUJ ) is rendered as a surface, and a loop interest, our approach is to create different protein fusions of PA that will alter the crystal packing structure of PA, which could allow the visualization of the apo protein through
534 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)
535 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
536 5j3b - The translation elongation factor P in actinobacteria 2020 B Pinheiro Damasceno Florentino - 2020 - edoc.ub.uni-muenchen.de NC Nascent peptide-chain ORF Open reading frame PCR Polymerase chain reaction PDB Protein data EF- P facilitates translation of XPPX motifs is based in many structural studies... Structural superposition and ribbon representations of available EF-P structures. C. glutamicum (PDB code 6S8Z, orange, this work), Acinetobacter baumannii (PDB code: 5J3B, blue), E. coli (
537 6mb1 - Profiling of myristoylation in Toxoplasma gondii reveals an N-myristoylated protein important for host cell penetration 2020 M Broncel, C Dominicus, L Vigetti, SD Nofal, EJ Bartlett- Elife, 2020 - elifesciences.org structure with bound IMP-1002 ( PDB : 6MB1 , [Schlott et al., 2019]) revealed high sequence identity (57%) and showed that all residues directly involved in compound binding are conserved within the TgNMT active site and therefore predicted to adopt an identical structural
538 6c9e - Molecular and shell biologyexamining the biochemistry and physiology of prokaryotic nanocompartments 2020 RJ Nichols - 2020 - escholarship.org (B) Size comparison of the nanocompartments to GFP [ PDB : 1C4F], the HK97 viral capsid [ PDB : 1OHG], and the Lastly, given that there is no known structure of a DyP- packaging encapsulin, these nanocompartments may have a pore architecture that permits transit
539 5cc8 - Transition from classical methods to new strategies: Mechanistic evaluation of inhibitors against Mycobacterium tuberculosis shikimate kinase 2018 N Ren Fuanta - 2018 - etd.auburn.edu of each family. As stated previously, structural information and interactions with substrate(s) or Group Family and members Example Structure Group 1: Protein S/TY kinase/ atypical protein kinase/ lipid kinase/ ATP- grasp Thiamine-monophosphate kinase PDB : 5CC8 (50)
540 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).. ...
541 5dvw - Evolutionary Trends in Viral Pathogens within and between Outbreaks 2017 ME Saha - 2017 - etd.ohiolink.edu for VP35 the 3FKE and 4YPI maps were used. For the other VP proteins: maps 4LDD and 4LDB for VP40, maps 2I8B and 5DVW
542 5ez3 - Characterization of sulfated polysaccharide activity against virulent Plasmodium falciparum PHISTb/RLP1 protein 2020 JM Mutisya, VA Mobegi, JK Kinyua, MN Kivecu- , 2020 - f1000research.com sequences to the reference, 12 non-synonymous single nucleotide polymorphisms were considered for mutant protein structure analysis. Eleven drug compounds with antiplasmodial activity were identified. Both modelled PHISTb/RLP1 reference and mutant structures had a
543 5idw - Structure and characterization of a NAD(P)Hdependent carbonyl reductase from Pseudomonas aeruginosa PAO1 2017 S Li, X Teng, L Su, G Mao, Y Xu, T Li, R Liu- FEBS, 2017 - Wiley Online Library NADP binding induces structural changes including the ordering of the active site specificity loop, and the presence of small molecules The native PA4079 structure was determined by molecular replacement with phaser 14 in the phenix suite 15 using PDB entry 3WXB
544 4weo - Rational design of Meso2,3butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations 2017 Z Pu, F Ji, J Wang, Y Zhang, W Sun, Y Bao- FEBS letters, 2017 - Wiley Online Library (A) Structure superposition of the BDHs in Protein Data Bank ( PDB code 1GEG: cyan; 3A28: green; 3WYE: yellow; 4WEO : red). (B) Sequence alignment between the four BDHs. It was prepared with the program Espript 3.0 (http://espript.ibcp.fr)
545 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
546 4ix8 - Bioinformatic analysis of the fold type I PLPdependent enzymes reveals determinants of reaction specificity in lthreonine aldolase from Aeromonas jandaei 2018 K Fesko, D Suplatov, V vedas- FEBS open bio, 2018 - Wiley Online Library to account for structural and functional variability within a large superfamily. First, comparison of protein structures was implemented to study distant evolutionary relationships because structures are more conserved in evolution than sequences. Table 1. Conserved and FSPs in the aspartate aminotransferase superfamily. Tyrosine aminotransferase 4ix8 D253
547 4ix8 - Biochemical and structural characterization of tyrosine aminotransferase suggests broad substrate specificity and a two state folding mechanism in Leishmania 2019 S Sasidharan, P Saudagar- FEBS Open Bio, 2019 - Wiley Online Library outlier region. PROSA score of PM0081305 was -8.56 and the score remained in the region of known native structures . The template structure that was taken for modeling ( PDB ID: 4IX8 ) had a PROSA score of -8.89. The structure
548 5cy4 - Characterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular disulfide bond for homodimer formation and nuclease activity 2019 Y Piotrowski, K Berg, DP Klebl, I Leiros- FEBS open, 2019 - Wiley Online Library campestris, PDB 1J9A: Haemophilus influenzae, PDB 2IGI: E. coli, PDB 3TR8: Coxiella burnetii, PDB 5CY4 : Acinetobacter baumannii) In the X. campestris Orn structure ( PDB 2GBZ) it is shown that Orn forms a dimer in the crystal From the structural analysis it was shown that
549 5vn4 - Crystal structures of APRT from Francisella tularensis an NHN hydrogen bond imparts adenine specificity in adenine phosporibosyltransferases 2018 GC Pavithra, UA Ramagopal- The FEBS journal, 2018 - Wiley Online Library [2]. The structure along with core PRPP binding domain also possesses a catalytic loop It should be noted that the overall architecture of FtAPRT is very similar to that of other canonical APRTs ( PDB -1QB7) [4] and Trypanosoma brucei ( PDB - 5VN4 ) with a C-terminal extension
550 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
551 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
552 4egq 4egj, 4eg0 Burkholderiapseudomallei dalaninedalanine ligase; detailed characterisation and assessment of a potential antibiotic drug target 2019 L DazSez, LS Torrie, SP McElroy, D Gray- The FEBS, 2019 - Wiley Online Library An apo-BpDdl structure ( PDB code 4EGQ ) has been determined by the Seattle Structural Genomics Center for Infectious Disease. Electron and difference density maps in the ATP binding sites were inspected to ascertain if a ligand might be present
553 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 )
554 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
555 5vpq - Conserved residues Glu37 and Trp229 play an essential role in protein folding of lactamase 2021 A Chikunova, MP Manley, M Ud Din Ahmad- The FEBS, 2021 - Wiley Online Library (2013). Cation- Interactions in -Lactamases: The Role in Structural Stability, Cell Biochem. Biophys. 66, 147155 [49] RP Joosten, F. Long, GN Murshudov & A. Perrakis. (2014). The PDB -REDO server for macromolecular structure model optimization, IUCrJ. 1, 213220 ... Pro226-Trp229-Pro251-Pro252-(Phe287) chain: β-lactamase from Burkholderia phymatum—gold (5VPQ), ...
556 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
557 5eqz - Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization 2017 A Ouali, D Allouche, S De Givry- on Uncertainty in, 2017 - hal.archives-ouvertes.fr Variable Neighborhood Search (VNS) (Mladenovic and Hansen, 1997) is a metaheuristic that uses a finite set of pre-selected neighborhood structures Nk,k = 1, 2, ..., kmax to escape from local minima by system- atically changing the neighborhood structure if the cur- rent one
558 6wpt - Hyaluronic Acid-2-Deoxy-D-Glucose Conjugate Act as a Promising Targeted Drug Delivery Option for the Treatment of COVID-19 2021 R Thirumalaisamy, V Aroulmoji- International, 2021 - hal.archives-ouvertes.fr of 2DG and HA-2DG was submitted to Online SMILES convertor and Structure file generator proteases Mpro (6LU7), papain like protease PLpro (6W9C), spike protein ( 6WPT ), RNA dependent RNA polymerase (6M71) was retrieved from RCSB PDB database (https
559 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 ...
560 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 ...
561 6nb3 6q04 Molecular mechanisms behind anti SARS-CoV-2 action of lactoferrin 2021 M Miotto, L Di Rienzo, L B- Frontiers in, 2021 - internal-journal.frontiersin.org Structural studies determined the structures of such protein both in free form and bound to ACE2 of the ACE2 receptor with SARS-CoV-2 spike receptor-binding domain, RBD ( PDB id: 6m17 ... The 10 structural analogs (as identified by TM-align Zhang and Skolnick (2005)) found by I-tasser are PDB id: 5X58, 6NZK, 6NB3, 3JCL, 5I08, 6CV0, 5SZS, 5WRG , 6UTK, 6B7N. The first (out of five) model returned
562 4mpq - Structural Characterisation of members of the DHDPS/NAL subfamily of proteins 2017 C MacDonald - 2017 - ir.canterbury.ac.nz 2HMC A. tumefaciens HypD 4MPQ B. melitensis HypD p(r) Pair distribution function plot pdb Protein data base This information is displayed using espript software (Robert and Gouet 2014) with secondary structure of E. coli DHDPS being shown along the top
563 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
564 4odj 4h3z, 4kgn, 4ig6 Static and dynamic properties of knotted biopolymers: from bulk to nanochannels and nanopores 2017 A Suma - 2017 - iris.sissa.it ... Several pioneering experiments and structural surveys demonstrated that knots can appear in biopolymers such as RNA [7], proteins [8 ... PDB download (~105 protein chains) ... We have used the same cutoff distance to check if some structure , such as the cyclotide, had a cyclized ...
565 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
566 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
567 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
568 4o3v - Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis 2019 I Tuvi-Arad, G Alon- Journal of cheminformatics, 2019 - jcheminf.biomedcentral.com model of allostery (also referred to as the symmetry model) [5]. Synthesizing a symmetric structure requires less is a characteristic of many protein structures [7]. Searching the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB ) [8, 9] for
569 5b8i - In Vitro and In Vivo Assessment of FK506 Analogs as Novel Antifungal Drug Candidates 2018 Y Lee, KT Lee, SJ Lee, JY Beom- Antimicrobial agents, 2018 - Am Soc Microbiol However, the structure of the fungal ternary complex from Coccidioides immitis has recently been reported ( PDB accession number 5B8I ), which would facilitate the rational design of FK506 analogs that can discriminate human and fungal calcineurins
570 4wbs - Structural modeling of the Treponema pallidum OMPeome: a roadmap for deconvolution of syphilis pathogenesis and development of a syphilis vaccine 2021 KL Hawley, JM Montezuma-Rusca- Journal of, 2021 - Am Soc Microbiol TP0786 Phyre2 LptB; Burkholderia phymatum; 4WBS 50 conserved in T. pallidum BamA, we performed structure -based sequence alignment of the 170 TP0326 3D model with the crystal structures of E. coli BamA ( PDB ID: 5D0Q, 5D0O) (60). The 171
571 5eks - Structural and biochemical analyses reveal that chlorogenic acid inhibits the shikimate pathway 2020 N Neetu, M Katiki, A Dev, S Gaur, S Tomar- Journal of, 2020 - Am Soc Microbiol replacement method using the coordinates of chain A of DHQS enzyme from Vibrio cholerae ( PDB identifier [ID]: 3OKF Structural comparison of PaDHQS structure with its homologs closer to its homologs from A. nidulans (1SG6), V. cholerae (3OKF), A. baumannii ( 5EKS ), and H
572 6bfu - Cryo-electron microscopy structure of the swine acute diarrhea syndrome coronavirus spike glycoprotein provides insights into evolution of unique coronavirus spike 2020 H Guan, Y Wang, V Perulija, AFUH Saeed- Journal of, 2020 - Am Soc Microbiol HCoV-NL63 ( PDB accession number 5SZS); (C) S trimer of the deltacoronavirus PdCoV ( PDB accession number 6BFU ); (D) S bronchitis virus (IBV) ( PDB accession number 6CV0); (E) S trimer of the betacoronavirus SARS-CoV ( PDB accession number 5X58 (F) Structure of the
573 6bfu - Insight into Vaccine Development for Alphacoronaviruses Based on Structural and Immunological Analyses of Spike Proteins 2021 Y Shi, J Shi, L Sun, Y Tan, G Wang, F Guo- Journal of, 2021 - Am Soc Microbiol (B) Overall structure comparison of coronavirus S-trimers. The S-trimer structures of HCoV-229E ( PDB ID: 6U7H), HCoV-NL63 ( PDB ID: 5SZS), PEDV ( PDB ID: 6U7K), FIPV ( PDB ID: 6JX7), PDCoV ( PDB ID: 6BFU ), IBV ( PDB ID: 6CV0), SARS-CoV ( PDB ID: 5X5B), SARS
574 4odj - A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs) 2018 C Ehrt, T Brinkjost, O Koch- PLoS computational biology, 2018 - journals.plos.org In parallel with the ever increasing number of available protein structures in the Protein Data Bank ( PDB )[1], various in silico techniques were developed to apply this structural knowledge[2]. In addition to molecular docking, structure -based pharmacophore searches, and
575 5vm8 - Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites 2020 AP Perlinska, A Stasiulewicz- PLOS Computational, 2020 - journals.plos.org depicted with rainbow coloring (TrmD, PDB ID: 4yvg), (B) unknotted methyltransferase (Trm5, PDB ID: 2zzm On the top of this it was shown that the structure of the knotted core Different conformations of the ligand imply differences in both structural and chemical characteristics of
576 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)
577 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
578 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.
579 6n41 - Whole-genome sequencing reveals origin and evolution of influenza A (H1N1) pdm09 viruses in Lincang, China, from 2014 to 2018 2020 XN Zhao, HJ Zhang, D Li, JN Zhou, YY Chen, YH Sun- PloS one, 2020 - journals.plos.org We searched and obtained the model template ( PDB ID: 6n41 .1.A) of HA protein of A/California/07/2009. We conducted a structure prediction of the trimeric HA protein by SWISS-MODEL, then the changes at the epitopes and RBSs were visualized in PyMol
580 4dz4 - Structure of the E. coli agmatinase, SPEB 2021 I Chitrakar, SF Ahmed, AT Torelli, JB French- Plos one, 2021 - journals.plos.org The first stage used the default parameters with the structure of Burkholderia thailandensis hypothetical agmatinase ( 4DZ4 ) [34] as To place the ligand in the SPEB active site, the structure of the D. radiodurans agmatinase with bound hexane-1,6-diamine ( PDB code 1WOG
581 6x79 7jv2 Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors 2021 Baysal, N Abdul Ghafoor, RS Silme, AN Ignatov- PloS one, 2021 - journals.plos.org The 3' end of the genome encodes 4 major structural proteins, including the spike protein (S), the nucleocapsid protein structure of refusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation ( PDB : 6X79 ), and X-ray diffraction structure of SARS
582 6wsa 4ghk, 4rgb, 3sgw, 4w5k, 3kcq, 3oxk, 3ppi Principal component analysis of alpha-helix deformations in transmembrane proteins 2021 A Bevacqua, S Bakshi, Y Xia- PloS one, 2021 - journals.plos.org 6tt4, 6txw, 6tzj, 6uqw, 6v47, 6vbj, 6vie, 6vjd, 6vmz, 6vnw, 6w1w, 6w2x, 6wok, 6wsa , 6x1q, 6x2m and the contribution of each physical deformation to the overall flexibility of the secondary structure N -helices of a given length (L residues) were collected from PDB entries (See
583 6q06 - Convergent structural features of respiratory syncytial virus neutralizing antibodies and plasticity of the site V epitope on prefusion F 2020 W Harshbarger, S Tian, N Wahome, A Balsaraf- PLoS, 2020 - journals.plos.org ]To fully elucidate the RSB1 paratope and the targeted PreF epitope architecture and better understand the competition with multiple antigenic sites, we determined the crystal structure of the ... Surface potential around PreF residue Asn200 from the structure of RSV B PreF PDB 6Q06 (left), with the RSB1 interacting residue Arg53(LCDR2) is shown again for comparison
584 4gl8 - Host-specific functional compartmentalization within the oligopeptide transporter during the Borrelia burgdorferi enzootic cycle 2021 AM Groshong, MA McLain, JD Radolf- PLoS pathogens, 2021 - journals.plos.org Structural homology models demonstrated variations within the binding pockets of OppA1, 2, and 5 indicative of different peptide repertoires We used larval immersion feeding [43] to confirm that oppA1 is essential for structural integrity of the spirochete during the blood meal
585 6bla - Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step 2020 X Ye, H Su, D Wrapp, DC Freed, F Li, Z Yuan- PLoS, 2020 - journals.plos.org A 1.8 crystal structure of 325 Fab in complex with the peptide epitope revealed the molecular determinants of 325 binding to gB A molecular replacement solution was found in PHASER [67] by using a search ensemble generated from PDB IDs: 6BLA and 6DDM.
586 6nb7 6nb4 Molecular mechanism for antibody-dependent enhancement of coronavirus entry 2019 Y Wan, J Shang, S Sun, W Tai, J Chen, Q Geng- Journal of, 2019 - Am Soc Microbiol change of the spike. Future study on the high-resolution cryo-EM structure of MERS- 230 CoV Se trimer complexed with Mersmab1 will be needed to provide detailed structural 231 information for the Mersmab1-triggered conformational changes of MERS-CoV Se. SARS-CoV S-e complexed with S230 mAb (PDB ID: 6NB7).
587 6bfu - Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins 2021 Y Shi, J Shi, L Sun, Y Tan, G Wang, F Guo- Journal of, 2021 - Am Soc Microbiol recognition pattern, especially the structure of the RBD and its state in the S-trimer, 112 Structural and immunological analyses of alpha- and beta-coronaviruses spike 124 proteins 125 To date, multiple S-trimer structures of coronaviruses have been resolved (12-14, 126
588 5eo6 4exq, 4wsh Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product 2017 A Bailey, R Webster, R Hunter, N Freemantle, G Rait - 2017 - Microbiol Mol Biol Rev The crystal structure of the P. aeruginosa enzyme shows that it is composed of Interestingly, crystal structures of P. aeruginosa variants with cysteine substitutions show decreasing Although structural information on porphobilinogen synthases from many sources shows that the
589 4gl8 - INVESTIGATION OF THE LIPOPROTEOME OF THE LYME DISEASE BACTERIUM BORRELIA BURGDORFERI 2017 AS Dowdell - 2017 - kuscholarworks.ku.edu lipoproteins, such as OspA (88, 89). Structural analysis of Lp6.6 showed that it exists primarily in aggregation-prone -helices and disordered stretches, and it is hypothesized that its unconstrained tertiary structure may be important for its biological role (90). Another similarly
590 4j07 - Strategies to improve the immunogenicity of subunit vaccine candidates 2018 Y Wei - 2018 - kuscholarworks.ku.edu Oligomeric state of lumazine synthase Quaternary structure Organism PDB ID Pentamer 1DI0 2F59 ; 2I0F 2OBX 2O6H 2JFB 1C41 2VI5; 2C9B; 2C92; 2C94; 2C97; 2C9D; 1W19; 1W29 4J07 1EJB 1KYV; 1KYX; 1KYY Decamer Brucella spp
591 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
592 6nb3 6vxx, 6vyb, 6nb6, 6nb4, 6nb7 Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel 2020 I Mercurio, V Tragni, F Busto, A De Grassi- Cellular and Molecular, 2020 - Springer Download PDF. Download PDF. Original Article; Published: 04 July 2020. Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies
593 4dq8 - Green synthesis, antitubercular evaluation, and molecular docking studies of ethyl 3, 5-dicyano-6-oxo-2, 4-diarylpiperidine-3-carboxylate derivatives 2020 T Sekhar, P Thriveni, K Ramesh, PG Prasad- Medicinal Chemistry, 2020 - Springer Full size image. Fig. 4 figure4. a 3D structure view of molecular docking of compound 4c (green sticks) with Mycobacterium AckA protein (gray lines) The PDB file of the target protein downloaded from RCSB PDB (www.rcsb.org), AckA (PDBID: 4DQ8 )
594 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
595 4ni5 - Crystal structure and iterative saturation mutagenesis of ChKRED20 for expanded catalytic scope 2017 FJ Zhao, Y Jin, Z Liu, C Guo, TB Li, ZY Li- Applied Microbiology, 2017 - Springer ... model was the monomer of Dehydrogenase from Brucella Suis ( PDB code 4NI5 ; NCBI accession ... Therefore, the determination of the crystal structure of ChKRED20 is crucial and greatly facilitates the ... high level of identity of ChKRED20 to typical SDRs in the PDB database, such ...
596 4z9n - Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics 2018 M Otzen, C Palacio, DB Janssen- Applied microbiology and biotechnology, 2018 - Springer 4282 5 1154 Acyl-CoA dehydrogenase 42, Thermus thermophilus 1.3.99.2 2DVL 2532 28 1031 ABC transporter, amino acid binding protein 59, Brucella ovis 4Z9N 3504 39 1922 Serine protein kinase 77, E. coli 2.7.11.1 P0ACY5
597 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
598 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
599 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
600 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 ...
601 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
602 4k9d - Identification and characterization of glyceraldehyde 3-phosphate dehydrogenase from Fasciola gigantica 2019 PB Chetri, R Shukla, T Tripathi- Parasitology research, 2019 - Springer homologs, and the structure of the GAPDH of Brugia Malayi ( PDB ID: 4K9D ) was selected After validation, the modeled structure was used for binding site prediction. The binding site was predicted using the PDB structure co-crystallized with substrate and cofactor (Frayne et al
603 6q04 - A comparative study of human betacoronavirus spike proteins: structure, function and therapeutics 2021 J Verma, N Subbarao- Archives of virology, 2021 - Springer Coronaviruses are the paradigm of emerging 21st century zoonotic viruses, triggering numerous outbreaks and a severe global health crisis. The current COVI.
604 4w91 - Ironsulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding 2017 J Prard, SO de Choudens- JBIC Journal of Biological Inorganic, 2017 - Springer Structural and biophysical analyses of Suf proteins SufS There are five crystal structures of SufS protein ( PDB numbers: 5J8Q; 4W91 ; 1T3I; 5DB5; 1I29) whose three published (Fig. 4) [7173]. The first crystal structure was Fig. 4 Overview of Suf protein structures SufS 1I29
605 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
606 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
607 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
608 5ucm - Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase 2020 J Zajac, H Anderson, L Adams, D Wangmo, S Suhail- The Protein, 2020 - Springer Identifying and understanding how these catalytic residues help enzymes achieve enormous rate enhancement has been the focus of many structural and biochemical studies over the past several decades Fig. 1 figure1. Structural model of E. coli ProRS
609 4kzk - Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus 2021 JE Bae, IJ Kim, Y Xu, KH Nam- The protein journal, 2021 - Springer of RmSBP, we performed comparative analysis and substrate docking studies using a previously reported crystal structure of SBP ( PDB code 5Z6V) as the initial model structure Among them, 9 models ( PDB codes: 3LFT, 2QH8, 5ER3, 4RS3, 4KZK , 5BRA, 3KSM, 2DRI
610 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
611 4f4f 3v7n Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major 2020 RJ Meshram, KT Bagul, SU Aouti, AM Shirsath- Molecular Diversity, 2020 - Springer conformational changes. Moreover, we address some important structural and dynamic interactions in the PLP binding region of TS that are in good agreement with previously speculated crystallographic estimations. Additionally
612 6vyb - Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination 2020 SA Ahmed, DA Abdelrheem, HR Abd El-Mageed- Structural Chemistry, 2020 - Springer Protein preparation. The 3D crystal structure of the SARS-CoV-2 main protease Mpro ( PDB ID: 6LU7) and the cryo-electron microscopic structure of the SARS-CoV-2 spike protein Sp ( PDB ID: 6VYB ) were taken from the PDB (Protein Data Bank) site
613 6vyb - Combination and tricombination therapy to destabilize the structural integrity of COVID-19 by some bioactive compounds with antiviral drugs: insights from 2021 HR Abd El-Mageed, DA Abdelrheem, SA Ahmed- Structural Chemistry, 2021 - Springer SARS-CoV-2 main protease ( PDB ID: 6LU7), (5b) SARS-CoV-2 spike protein domain ( PDB ID: 6VYB ), and (5c) human entry receptor ACE2 ( PDB ID: 1R42 validation was carried out using our previously published work [36] with re-docking of the co-crystal structure (N3) as an
614 6c49 - In silico study of the structure and ligand interactions of alcohol dehydrogenase from cyanobacterium Synechocystis Sp. PCC 6803 as a key enzyme for biofuel 2020 O Haghighi, M Moradi- Applied Biochemistry and Biotechnology, 2020 - Springer with amino acids in Zn ion binding sites along with a slight deviation between Cys 110 in the template and Cys 106 in the homology model in the location of structural Zn PCC 6803 homology model (Cyan) superimposed onto the template crystal structure ( PDB ID: 6C49 ) (Tan
615 4ege - Trichomonas vaginalis metalloproteinase TvMP50 is a monomeric Aminopeptidase P-like enzyme 2018 R Arreola, JL Villalpando, J Puente-Rivera- Molecular, 2018 - Springer Superposition with E. coli Prolidase Structure ( PDB : 4QR8) 4EGE and 4QR8 are dimers but 4EGE contains a CRE_N domain in the N-terminal determined N-terminal domain; however, as we showed in this study, this domain maintains a closely related architecture with AMP_N
616 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
617 5viu - Identification and expression profiling of proline metabolizing genes in Arabidopsis thaliana and Oryza sativa to reveal their stress-specific transcript alteration 2021 S Arabia, MNA Shah, AA Sami, A Ghosh- Physiology and Molecular, 2021 - Springer 2020) to stabilize the intracellular environment as well as the structures of proteins, membranes, and subcellular organelles (Verslues et al Data retrieval from Arabidopsis and Rice genome databases, and construction of gene structure and domain architecture
618 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
619 4q04 - Structural and functional diversity of Entamoeba histolytica calcium-binding proteins 2020 S Kumar, S Mishra, S Gourinath- Biophysical Reviews, 2020 - Springer 78% identical). Here, along with the reported structures of amoebic CaBP1, CaBP2, CaBP3, and CaBP5, we have complied the structural information of an unpublished structure of EhCaBP19 ( PDB deposited) as well. In this
620 5hxa - Cloning and expression analysis of tps, and cryopreservation research of trehalose from Antarctic strain Pseudozyma sp. 2017 H Yin, Y Wang, Y He, L Xing, X Zhang, S Wang, X Qi- 3 Biotech, 2017 - Springer of NJ7 was similar to the alpha, alpha-trehalose-phosphate synthase of 5hxa .1 (Mayclin were drawn into ten frames, which played important roles in maintaining the structure and function It can also act as a sensing compound, growth regulator and structural component of cell
621 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
622 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
623 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
624 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
625 6bfu - Glycosylator: a Python framework for the rapid modeling of glycans 2019 T Lemmin, C Soto- BMC bioinformatics, 2019 - Springer 1 ha0. 5fyl (gp120). 6bfu . Number of sequons. 6 A second N-Acetyl-D-Glucosamine will then be linked through a 1-4 glycosidic bond. Finally, an Alpha-D-Mannosewill be built ab initio and saved to a PDB file The structure of a mannose 9 will be imported as a Molecule instance
626 4g5d - Leishmania braziliensis prostaglandin F2 synthase impacts host infection 2020 EVC Alves-Ferreira, TR Ferreira, P Walrad, PM Kaye- Parasites & vectors, 2020 - Springer 1b) and the 3D structure (Fig c 3D sequence alignments of protein sequences of LmjPGF2S (PBD ID 4G5D , in grey) and human ortholog 51.4% similarity and 34.3% identity, modelling using the Research Collaboratory for Structural Bioinformatics (RCSB) PDB suggests that
627 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 ...
628 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
629 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]
630 5w25 - Impact of Target-Based Drug Design in Anti-bacterial Drug Discovery for the Treatment of Tuberculosis 2019 AC Pushkaran, R Biswas, CG Mohan- Structural Bioinformatics, 2019 - Springer Table 3 Crystal structure of the key druggable targets in Mtb. Molecular target. Pathways involved. PDB ID. DprE1. Arabinogalactan biosynthesis AspS. Protein synthesis. 5W25 . Peptide Deformylase. Maturation of nascent polypeptides. 3E3U. DNA Gyrase
631 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
632 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
633 4mei 4jf8, 4lso, 4kz1, 4o3v, 4nhf Structural and Molecular Biology of Type IV Secretion Systems 2017 L Terradot, C Berg, G Waksman- Type IV Secretion in Gram-Negative, 2017 - Springer 1.2 Composition of T4SSs. X-ray crystallography, nuclear magnetic resonance (NMR), and more recently electron microscopy have been successfully used to provide insights into the structure of T4SSs Plasmid or bacteria. PDB or EMDB ID 4KZ1,4JF8,4LSO, 4MEI ,4NHF m
634 4dz4 3dah, 5w15, 3t3w, 3inn, 3hm0, 3ld9, 3l0g, 3tk8, 3swo, 3slg, 3i3f, 4lgo, 5udf, 4ghk, 5kak, 4lgv, 5bq2, 4pca, 4q1t, 5dle Homo Multimer Protein Complexes 2018 P Kangueane, C Nilofer- Protein-Protein and Domain-Domain Interactions, 2018 - Springer 3T3W, 3T94, 3VZD, 3WCM, 3WSG, 3WU4, 4BLP, 4BLQ, 4C01, 4C9S, 4D2E, 4DZ4 , 4FLN, 4FZQ Distribution of homo multimer protein complex structures at the protein data bank ( PDB ) Structure of a homo trimer glycosidase (1AM7) from enterobacteria phage lambda is shown
635 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
636 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
637 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
638 4g7f 4iv5, 4fzi, 4lsm Synthesis of new N,S-acetal analogs derived from juglone with cytotoxic activity against Trypanossoma cruzi 2020 PAF Pacheco, T de Menezes Ribeiro- Journal of Bioenergetics, 2020 - Springer Naphthoquinones are considered important structures in medicinal chemistry due to their synthetic versatility and their v.1.0.1 program was used to build the molec- ular structure of ligands the best SI value among all molecules tested indicating that this structural feature might
639 4xgi - Homology Modeling and Molecular Docking Studies of Glutamate Dehydrogenase (GDH) from Cyanobacterium Synechocystis sp. PCC 6803 2019 O Haghighi, S Davaeifar, HS Zahiri, H Maleki- International Journal of, 2019 - Springer aLigand name in structure : NAD-507 Docking pose number Reference ligand in crystallography structure (ligand name and pdb code) NADH NADPH AKG Glutamate 1V9L 1HWYa 5GUD 5IJZ 1HWY 4XGI 6DHM 3AOG Pose 01 4.57 3.48 5.74 5.75 2.22 2.11 1.72 1.58
640 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
641 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
642 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
643 4ix8 - Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies 2021 D Suplatov, Y Sharapova, V vedas- Multiple Sequence Alignment, 2021 - Springer etc.): 3WGB, 2W7E, 3A2B, 1IBJ, 1LKC, 1 V72, 2BKW, 2EZ2, 4IX8 , 1QZ9, 4BA5 The missing loop regions in these PDB structures were reconstructed using the MODELLER software [23] enzymes, the MATT algorithm was used to prepare the initial 3D- structure superimposition of -- This is not a duplicate of their earlier 2018 work
644 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]
645 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
646 4qhq - Navigating Among Known Structures in Protein Space 2019 A Narunsky, N Ben-Tal, R Kolodny- Computational Methods in Protein, 2019 - Springer evolutionary history, with sequences that diverged beyond the point where one can identify their common ancestry; for example, the SCOP fold, CATH Architecture , and ECOD As both neighbors ( pdb 4qhq and pdb 3qwl) have a bound methionine in their PDB structure (Fig
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 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. ...
649 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
650 4mow - Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase 2016 AM de las Heras - Microbial Cell , 2016 - microbialcellfactories.biomedcentral. ... Since the crystal structures of these AARs were not available, protein structures were made ... protein sequence identity to the C. necator AAR whose crystal structure was used ... Both S. wolfei homology models (Swol_0651 modelled on PDB: 4MOW [27] and Swol_1910 modelled ...
651 5cy4 - A functional and structural study of three bacterial nucleic acid-interacting proteins. The story of a Ferric Uptake Regulator, an Oligoribonuclease and an ATP 2020 K Berg - 2020 - munin.uit.no Acinetobacter baumannii (PDB 5CY4) and E. coli (PDB code 1YTA )[148]. All Orn homologs are structurally similar and topologically arranged
652 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
653 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.
654 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
655 5jy1 - Clean Enzymatic Oxidation of 12Hydroxysteroids to 12OxoDerivatives Catalyzed by Hydroxysteroid Dehydrogenase 2019 F Tonin, N Alvarenga, JZ Ye- Advanced Synthesis, 2019 - Wiley Online Library MODEL (https://swissmodel.expasy.org/ interactive), employing the crystal structure of the putative SDR from Burkholderia xenovorans ( PDB ID: 5JY1 .1) as determination of the cosubstrate specificity of these enzymes.[11] The 3D model of the El12-HSDH structure showed a
656 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
657 4y0e - Pathway from Nalkylglycine to alkylisonitrile catalyzed by iron (II) and 2oxoglutarate dependent oxygenases 2020 WC Chang, TY Chen, J Chen, Y Tang- Angewandte, 2020 - Wiley Online Library Table S4). Dali search suggested the structure of ScoE resembles those of other Fe/2OG-enzymes such as CarC ( PDB ID: 4oj8) and a putative dioxygenases ( PDB ID: 4y0e ), with Z-score of 20.0 and 26.7, respectively. In the
658 4odj - Engineered SAM synthetases for enzymatic generation of AdoMet analogs with photocaging groups and reversible DNA modification in cascade reactions 2020 F Michailidou, N Klcker- Angewandte Chemie, 2020 - Wiley Online Library Figure 3. A) Superimposed structures of WT-ChMAT ( 4ODJ , shown in yellow) with product bound PC-ChMAT (6LTV, shown in grey) and share a sequence identity of 51% and are highly conserved in the active site (Figure S17), and our structure of PC-ChMAT ( PDB ID: 6LTV
659 4f2n - Antileismanial activity, mechanism of action study and molecular docking of 1, 4bis (substituted benzalhydrazino) phthalazines 2019 AH Romero, N Rodrguez, H Oviedo- Archiv der, 2019 - Wiley Online Library candidate for further pharmacokinetic and in vivo experiments as antileishmanial agent, and as a platform for further structural optimization ... Representation of molecular docking of 1,4‐bis‐(substituted benzalhydrazino) phthalazine 3b on the superoxidedismutase active sites of Leishmania major (PDB code: 4F2N)
660 5k85 - Selective inhibition of Zophobas morio (Coleoptera: Tenebrionidae) luciferaselike enzyme luminescence by diclofenac and potential suitability for lightoff 2020 MC Carvalho, A Tomazini, RA Prado- Luminescence, 2020 - Wiley Online Library tertiaricarbonis PDB file ID: 6HE0, Cryptococcus neoformans PDB file ID: 5K85 , Salmonella typhimurium PDB file ID: 5JRH) indicated that, among the five binding sites, that of CoA was structure and function prediction. Nat Protoc 2010; 5: 25-738. 49
661 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
662 5b8h - Identification of Specific and Nonspecific Inhibitors of Bacillus anthracis TypeIII Pantothenate Kinase (PanK) 2019 JA Shapiro, JJ Varga, D Parsonage, W Walton- , 2019 - Wiley Online Library Organic synthesis of analogues along with biochemical validation of the proposed mechanism will allow structure function analysis and form 2H3G, DOI: 10.2210/pdb2H3G/ pdb ), PaPanK ( PDB ID: 2F9T, DOI: 10.2210/pdb2F9T/ pdb ), and BcPanK ( PDB ID: 5B8H , DOI: 10.2210
663 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
664 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
665 6brl - Metabolic impact of pathogenic variants in the mitochondrial glutamyltRNA synthetase EARS2 2021 M Ni, LF Black, C Pan, H Vu, J Pei, B Ko- Journal of Inherited, 2021 - Wiley Online Library 3A and B). Structural modeling of human EARS2 was obtained from the SWISS-MODEL Page 10. repository (Bienert et al 2017) based on the crystal structure of the glutamyl-tRNA synthetase from Elizabethkingia meningosepticum ( PDB : 6brl ), and superimposed on the crystal
666 5ha4 - In silico prediction, molecular docking and binding studies of acetaminophen and dexamethasone to Enterococcus faecalis diaminopimelate epimerase 2021 H Singh, S Das, J Yadav, VK Srivastava- Journal of Molecular, 2021 - Wiley Online Library are also available in the PDB , but are to date otherwise unpublished, including Acinetobacter baumannii ( PDB : 5HA4 ), Bacillus anthracis ( PDB : 2OTN structural and functional studies of DAP epimerase from different organisms have reported that the structure consists of
667 5vm1 - Heterologous expression and biochemical characterization of a thermostable xylulose kinase from Bacillus coagulans IPE22 2019 Y Zhang, C Zhao, Z Ni, M Shao, M Han- Journal of basic, 2019 - Wiley Online Library was shown in Figure 1. In the 3D structure modeling analysis, Bc-XK showed the highest sequence identity of 35% with the homologue from Brucella ovis ATCC 25840 ( PDB accession number 5VM1 , DOI: 10.2210/pdb5VM1/ pdb ), the confi- dence and structure coverage values
668 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
669 4yet 4f2n Tropical and Subtropical Parasitic Diseases: Targets for a New Approach to Virtual Screening 2019 MJR Yunta, RC Dietrich- Molecular informatics, 2019 - Wiley Online Library The most stable extended geometry was always used as the starting structure in all SODb2 (glycosomial), 2GOJ for Plasmodium Falci- parum Fe-SODb1 (cytosolic) and 4YET for Babesia Starting water molecules positions were those published in the corresponding PDB library
670 5vm8 - Crystal structure of the Legionella pneumophila Lpg2936 in complex with the cofactor SadenosylLmethionine reveals novel insights into the mechanism of RsmE 2017 N Pinotsis, G Waksman- Protein Science, 2017 - Wiley Online Library RsmE ( PDB ID 4e8b),[13] from H. influenzae ( PDB ID: 1nxz and 1vhy)[14] and from N. gonorrhoeae ( PDB ID 5vm8 ) Structure based sequence alignment using the most similar structures from seven different bacteria species reveals (i) a highly conserved C-terminal part of
671 4odj - CrossStrand Disulfides in the Hydrogen Bonding Site of Antiparallel sheet (aCSDhs): Forbidden Disulfides that are Highly Strained, Easily Broken 2018 NL Haworth, MJ Wouters, MO Hunter, L Ma- Protein, 2018 - Wiley Online Library Examples include interleukin 36 receptor antagonist (PDB: 1md6) and the previously mentioned ML domains. Other aCSDhs span only short segments of sequence straddling a β‐hairpin (PDBs: 5bvw, 3fl7, 1htd, 3ngm, 4odj).
672 6mfk - Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species 2019 A Alcala, G Ramirez, A Solis, Y Kim, K Tan- Protein, 2019 - Wiley Online Library from P. aeruginosa ( PDB IDs: 1XAT, 2XAT7) and E. anophelis ( PDB ID: 6MFK ). Known SAT 1(A)]. When we compared our structures of the Vibrio proteins with CATs and SATs from the PDB , we found the The AfCAT structure had
673 6ok4 - Chlamydia trachomatis glyceraldehyde 3phosphate dehydrogenase: Enzyme kinetics, highresolution crystal structure, and plasminogen binding 2020 N Schormann, J Campos, R Motamed- Protein, 2020 - Wiley Online Library Chlamydia trachomatis glyceraldehyde 3phosphate dehydrogenase: Enzyme kinetics, highresolution crystal structure , and plasminogen binding. Norbert Schormann We describe here the highresolution crystal structure of the holo enzyme refined at 1.5 resolution
674 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
675 5unb - Assessment of hard target modeling in CASP12 reveals an emerging role of alignmentbased contact prediction methods 2018 LA Abriata, GE Tam, B Monastyrskyy- Proteins: Structure, 2018 - Wiley Online Library T0878-D1, 18.30, 12.84, 25.44, 344, 0.85, Burkholderia thailandensis, 5unb Panel E shows the structure of the full target T0912, rainbow-colored to highlight the discontinuities of its Target T0866 ( PDB 5uw2, a homohexamer, Figure 2A) was assessed as 1 evaluation unit of the FM
676 4q15 - Development of METALACTIVE SITE and ZINCCLUSTER tool to predict active site pockets 2018 M Ajitha, K Sundar, S Arul Mugilan- Proteins: Structure, 2018 - Wiley Online Library As zinc ion acts as a cofactor for this protein, ZN and PDB ID (3CAJ) of this of Sobolev et al.,[14] who identified the presence of Zinc using three-dimensional structure and he 1Q15, 0.86, 2Q15, 0.86, 3Q15, 0.84, 4Q15 , 0.28, 5Q15, 0.86, 6Q15, 0.86, 7Q15, 8.86, 8Q15, 0.86, 9Q15
677 4whx - The transaminase engineering database (oTAED): a navigation tool in protein sequence and structure space 2018 O Bu, PCF Buchholz, M Grff- Proteins: Structure, 2018 - Wiley Online Library entry 4WHX ) and an amino lyase with activity towards 4-amino-4-deoxychorismate ( PDB entry 2Y4R) [68] as the -TA from Arthrobacter sp. ( PDB entries 5FR9 and 3WWH) which was adapted by John Wiley & Sons, Inc. PROTEINS: Structure , Function, and Bioinformatics
678 4ywj - Coil conversion to strand induced by dimerization 2018 J Laibe, A Caffrey, M Broutin, S Guiglion- Proteins: Structure, 2018 - Wiley Online Library CATH: an expanded resource to predict protein function through structure and sequence -strand interfaces, standard - strand interfaces and domains in CATH (based on PDB release: July 01 interface including a salt bridge between E226-A and H232-B ( 4YWJ ) B. Dimorphic
679 5elo 6aqg, 5vl1, 6c86 Side chain rotameric changes and backbone dynamics enable specific cladosporin binding in Plasmodium falciparum lysyltRNA synthetase 2019 J ChhibberGoel, A Sharma- Proteins: Structure, Function, and, 2019 - Wiley Online Library ( PDB : apo 6C86, holo 5ELO ) and M. ulcerans (MuKRS) ( PDB : apo 5VL1, holo re-arrangements and are noted as 1 to 4 for all the four PDB data sets (Table 1 and Fig. 1). In based on structural analyses. Our analyses also provide a platform for structure -guided
680 5el0 - An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. 2019 PI Koukos, J Roel-Touris, F Ambrosetti, C Geng- bioRxiv, 2019 - biorxiv.org For the server submission of target 134, we modelled the protein on PDB entry 4d07 and the peptide on 4d07 and 4qh8, threading the target sequence on the peptide structure of the templates 5el0 and followed similar strategies as for target 134. Template-based targets
681 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
682 6aqz - Crystal structure of a GDP6OMe4ketoLxyloheptose reductase from Campylobacter jejuni 2021 JH Kim, A Hofmann, JS Kim- Proteins: Structure, Function, and, 2021 - Wiley Online Library Page 9. Discussion Comparison with other related proteins The crystal structure of Camylobacter MlghC revealed a two-domain architecture commonly found in 36.7; rmsd 1.9 ) and Naegleria fowleri ( PDB ID 6AQZ ; Z-score 34.3; rmsd 2.3 ), and GDP-4-keto-6
683 5bnt - Structure of aspartate semialdehyde dehydrogenase from Francisella tularensis 2018 NJ Mank, S Pote, KA Majorek- Section F: Structural, 2018 - Wiley Online Library NADP+ (yellow spheres) is modeled using the structure of H. influenzae ASADH ( PDB PDB entry 3pzr; Pavlovsky et al., 2012), Pseudomonas aeruginosa ( PDB entry 5bnt ; Seattle Structural entry 1t4b; Nichols et al., 2004) and Haemophilus influenzae (HiASADH; PDB entry 1pqu
684 4nbr - MRREX: molecular replacement by cooperative conformational search and occupancy optimization on lowaccuracy protein models 2018 JJ Virtanen, Y Zhang- Acta Crystallographica Section D, 2018 - Wiley Online Library et al., 2016, 2017; Shrestha & Zhang, 2015), MR-REX takes advan- tage of this fact by predicting possible inaccurate segments of the structural model and Input and output data The input to MR-REX is a set consisting of structure -factor data, a structure file in PDB format and
685 6cum - Introduction to molecular replacement: a time perspective 2021 E Dodson- Acta Crystallographica Section D: Structural, 2021 - Wiley Online Library the phase error between the correct value and the phases generated from the best solution; Dphi_DM, the phase error after density modification, which was performed with Parrot, except for PDB entry 6cum , which used Rebuilt?, Yes if the test structure could be rebuilt
686 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
687 4zju - Ternary complex formation of AFN1252 with Acinetobacter baumannii FabI and NADH: Crystallographic and biochemical studies 2020 NK Rao, V Nataraj, M Ravi- Chemical Biology &, 2020 - Wiley Online Library 6AHE) with the NAD bound AbFabI ( PDB :4JZU) (243 C atoms; PDB ; 4ZJU ),showed an rms Structural superposition revealed no major conformational changes except in The crystal structure of AbFabI in the ternary complex is similar to the reported structures of EcFabI
688 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
689 5i7w - Characterization of Cystathionine Synthase TtCbs1 and Cysteine Synthase TtCsa1 Involved in Cysteine Biosynthesis in Tetrahymena thermophila 2020 H Lv, J Xu, T Bo, W Wang- Journal of Eukaryotic Microbiology, 2020 - Wiley Online Library TtCsa1 has more than 30% sequence identities with B. abortus CS ( PDB ID: 5JIS) (Dharavath et al. 2017), B. suis CS ( PDB ID: 5I7W ), and L. major CS ( PDB ID: 4AIR) (Fyfe et al. 2012), and we modeled the overall structure of TtCsa1 with these crystal structures
690 4zju - Structure and substrate specificity of ketoacylacyl carrier protein synthase III from Acinetobacter baumannii 2018 WC Lee, MC Jeong, Y Lee, C Kwak- Molecular, 2018 - Wiley Online Library detailed structures of FAS-related proteins from A. baumannii are still lacking except for the unpublished structure of FabI ( PDB ID: 4ZJU ). To our knowledge, the AbKAS III structures KAS III orthologs, whereas only one is found in the A. baumannii genome. Our structure and
691 4x54 - The mycolic acid reductase Rv2509 has distinct structural motifs and is essential for growth in slowgrowing mycobacteria 2020 A Javid, C Cooper, A Singh, S Schindler- Molecular, 2020 - Wiley Online Library structures of the four highest-scoring experimental SDRs (3ASU/3ASV, 1XG5, 4X54 and 4BMV based on the SDR from Sphingobium yanoikuyae (4BMV. pdb ; GenBank ID ACB78183.1 structure elements of Rv2509 aligned to its corynebacterial homologues, the core structure of
692 6ona - Evolution of H9N2 avian influenza viruses in Iran, 20172019 2020 M Bashashati, DH Chung- Transboundary and, 2020 - Wiley Online Library (http://www.cbs.dtu.dk/services/NetNGlyc/) and GlyProt server (http://www.glycosciences.de/ modeling/). The HA structure was modelled using the H9 HA template ( PDB accession number, 6ONA ) in the SWISS-MODEL server (https://swissmodel.expasy.org/) and
693 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).
694 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. ...
695 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
696 4giv - Investigating the molecular architecture of yeast histone acetyltransferase complexes 2016 D Setiaputra - 2016 - open.library.ubc.ca Learning, knowledge, research, insight: welcome to the world of UBC Library, the second-largest academic research library in Canada.
697 4g50 - Entwicklung von Inhibitoren des macrophage infectivity potentiator -Proteins 2016 F Seufert - opus.bibliothek.uni-wuerzburg.de ... Zur Evaluierung möglicher struktureller Verbesserungen von S-1a wurden auch für BpMip Hot- Spot- und Docking-Analysen von M. Hein und M. Kuhn vorgenommen. Dazu wurden die Strukturen PDB 4G50 bzw. 4GGQ75 für BpMip und 2VCD-4 für LpMip verwendet.. ...
698 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. ...
699 5unb - Janus kinase inhibition for autoinflammation in DNASE2 deficiency 2019 S Nanthapisal, A Cavounidis, H Takeshita- Journal of Allergy and, 2019 - ora.ox.ac.uk Structural modeling Structural models and figures were prepared by using the ICM software package (MolSoft, San Diego, Calif). A homology model for human DNase II was prepared by using the existing structure from B thailandensis ( PDB 5UNB ) as the model template
700 6pqh - Development of Novel Antibacterial Agents through the Design and Synthesis of Aminoacyl tRNA Synthetase (AaRS) Inhibitors 2020 H Asiri, C Simons, E Mantzourani - 2020 - orca.cf.ac.uk 33 Figure 16: Chemical structures of LysRS and AspRS inhibitors. 34 Figure 17: Chemical structures of AsnRS and AlaRS inhibitors. 34 Figure 21: 3D structure of Thermus thermophilus AsnRS ( pdb : 5ZG8) with two-8 amino acid residues gaps (161-168 and 209-216) identified. Table 7. Elizabethkingia anopheles 6PQH
701 5v6d - A Centipede Toxin Family Defines a New Ancient Class of CS Defensins 2018 TS Dash, T Shafee, PJ Harvey, C Zhang- Available at SSRN, 2018 - papers.ssrn.com structure of Sm2 against all structures of proteins contained within the Protein Data Bank ( PDB ) that are composed of more than 30 amino acids Thus, the minimal cysteine motif is by itself sufficient to generate a stable CS structure . Although the 2ds-CS architecture has
702 6bfu 6q04, 6tys, 6nb3, 6nb7, 6nb6 Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology-and bioinformatic-based predictions 2020 A Grifoni, J Sidney, Y Zhang- -HOST-MICROBE-D, 2020 - papers.ssrn.com with data about immune epitopes, protein structures , and host responses to virus infections (Pickett et al., 2012) glycoprotein structure ( PDB : 6ACD). The calculated surface of the top 10 amino acid residues Non- structural protein 3b 2 0 Protein 7a 2 0 Protein 9b 2 0
703 4g5d - Leishmania braziliensis prostaglandin F 2020 EVC AlvesFerreira, TR Ferreira, P Walrad - 2020 - parasitesandvectors.biomedcentral 1b) and the 3D structure (Fig c 3D sequence alignments of protein sequences of LmjPGF2S (PBD ID 4G5D , in grey) and human ortholog share 51.4% similarity and 34.3% identity, modelling using the Research Collabora- tory for Structural Bioinformatics (RCSB) PDB suggests
704 4efi - Methods for the site-selective introduction of halogen into natural products 2016 MCY Chang, MC Walker, BW Thuronyi- US Patent App. 14/913,601, 2016 - Google Patents domain. The NphT7 structure was predicted using Phyre2 (Kelley, et al., Nat. Prot., 4:363-371 (2009)) and based on a type III 3-oxoacyl-(acyl-carrier protein) synthase from Burkholderia xenovorans ( PDB ID 4EFI ). Despite
705 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
706 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
707 4ot8 - Chemoenzymatic synthesis of peptide beta-lactones and beta-hydroxy acids 2018 TA Wencewicz, JE Schaffer, MR Reck- US Patent App. 15/921,442, 2018 - Google Patents Although the biological target of RC-Obi is unknown, bacterial transpeptidases are thought to be potential targets due to the structural similarity of RC-Obi to monocyclic -lactam antibiotics and the FIG. 14D is an X-ray crystal structure of the EntF TE domain ( PDB 3TEJ). FIG
708 4dxl - Oxadiazole and phenol derivatives as antibacterial and/or herbicidal agents 2018 TJ Hagen, M Thompson, JR Troxell- US Patent App. 15, 2018 - Google Patents To date, there are 17 crystal structures of six different species of IspE deposited in the PDB with 17 different ligands FIG. 11 . X-Ray Crystal Structure of Mycobacterium abscessus IspE with ATP (red) and CMP (blue) Bound to Active Site; PDBID 4DXL . FIG. 12
709 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
710 5vwm - In silico study of various compounds from essential oil of Cymbopogon winterianus against Pseudomonas aeruginosa targets 2019 Moura, A Monteiro, M Maia, N Sousa, G Rodrigues - 2019 - pdfs.semanticscholar.org Protein resolution values were 2.1 for ExoA ( PDB ID 1XK9), 1.8 for LpxC ( PDB ID 5VWM ) and 2.31 for PBP3 ( PDB ID 4KQO). All presented inhibitors coupled to their crystallographic structure , which allowed the delimitation of the active site of each protein
711 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
712 6vyb - Comparative docking studies on curcumin with COVID-19 proteins 2020 R Suravajhala, A Parashar, B Malik, VA Nagaraj - 2020 - pdfs.semanticscholar.org were subjected to a 3D structure generation on CORINA [12] using their SMILE Preparation of proteins and grid parameters: The protein data bank ( PDB ) structures of different proteins were retrieved from RCSB membrane protein (6M17), polymerase (6M71), spike ( 6VYB )
713 5unb - Supplementary materials to PconsC4: fast, free, easy, and accurate contact predictions. 2018 M Michel, D Menndez-Hurtado, A Elofsson - 2018 - pdfs.semanticscholar.org PconsC4 is trained on a set of 2759 proteins culled from PDB using PISCES (Wang and in (Michel et al., 2017) and the 46 proteins from CASP12 with available structures , Table S6 It is pre-trained to predict secondary structure and surface accessibility for each residue (golden
714 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
715 5u9p 3ftp Electrical Supporting information 2018 F Sha, Y Zheng, J Chen, K Chen, F Cao, M Yan - pdfs.semanticscholar.org Entry Enzyme GenBank accession no. Amino acid identities with PspPDH [%] Template PDB code TM- scorea Gbind [kcal mol-1] 23 PhpPDH WP_045028254 41.53 4z9y 0.90 -5.71 1.96 24 DfPDH WP_050774712 31.98 5u9p 0.90 -11.90 2.01
716 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
717 4ywj 3ijp, 4f3y Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly 2018 SAJ Watkin, JR Keown, E Richards- Biochemical, 2018 - portlandpress.com DHDPR from a total of nine bacterial species, whereas no plant DHDPR structures were previously and X-ray crystallography to demonstrate how small elements of secondary structure are able Additionally, we use kinetic assays and an analysis of the structural flexibility of the
718 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)
719 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
720 4o5o - Engineering Erg10 Thiolase from Saccharomyces cerevisiae as a Synthetic Toolkit for the Production of Branched-Chain Alcohols 2018 P Torres-Salas, V Bernal, F Lopez-Gallego- Biochemistry, 2018 - ACS Publications Using a combined computational/experimental approach, and guided by structural information, we have studied the potential of thiolases to with novel properties, the naturally occurring metabolism of microorganisms is not always sufficient to obtain any desired structure
721 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
722 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
723 4hvt - Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase 2019 K Ellis-Guardiola, H Rui, RL Beckner, P Srivastava- Biochemistry, 2019 - ACS Publications Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase While extensive structural characterization of bacterial and mammalian POPs has been performed, no structures for archaeal POPs have been reported
724 4noz 4mh4 Substrate and product-assisted catalysis: molecular aspects behind structural switches along Organic Hydroperoxide Resistance Protein catalytic cycle 2020 R Mateus Domingos, RD Teixeira, A Zeida- ACS, 2020 - ACS Publications The Ohr active site architecture is composed of two cysteines structures (Figure S1). Notably, when analyzing the other Ohr structures available in the PDB , we observed that the position of the Arg-loop in the Bacillus subtilis OhrB (BsOhrB) structure presents an intermediate
725 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
726 4lgv - Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress 2019 GA Ellis, WP Klein, G Lasarte-Aragones, M Thakur- ACS, 2019 - ACS Publications Within each material class of scaffolds, attention is given to their inherent chemical diversity, how they are engineered, how they allow for enzymatic attachment, their ease of use, their benefits (eg, inherent three-dimensional architecture ) ... Illustration of the proposed channeling complex using a poly(lysine) bridge as an electrostatic surface between hexokinase (HK) (PDB entry 3VF6) and glucose-6-phosphate dehydrogenase (G6PDH) (PDB entry 4LGV).
727 4ohc - Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by means of X-ray Crystallography and Computational Simulations 2020 M Roca, S Navas-Yuste, K Zinovjev- ACS, 2020 - ACS Publications Then, the dimeric architecture of OPRTase plays an essential role in the catalysis since The coordinates and structure factors have been deposited in the Protein Data Bank ( PDB ) with accession codes 6TAI (EcOPRT), 6TAJ (EcOPRT/OA) and 6TAK (EcOPRT/OA/SO4 2-). 2.5
728 4iwh - Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data 2019 JT Seffernick, SR Harvey, VH Wysocki- ACS Central, 2019 - ACS Publications from which data have been favorably compared to known crystal structures on many along with other bioanalytical MS and dissociation techniques, yields useful structural information, the sparse, not allowing for an unambiguous determination of the protein complex structure... Additionally, the Pnear also improved for 56/57 ideal cases (except 4IWH) when SID data were used, as shown in Figure S3A.
729 4ot8 - l-Threonine Transaldolase Activity Is Enabled by a Persistent Catalytic Intermediate 2020 P Kumar, A Meza, JM Ellis, GA Carlson- ACS Chemical, 2020 - ACS Publications l-Threonine transaldolases (lTTAs) are a poorly characterized class of pyridoxal-5-phosphate (PLP) dependent enzymes responsible for the biosynthesis of diverse -hydroxy amino acids... The structure was solved by molecular replacement with a distantly related serine hydroxymethyltransferase (PDB ID: 4OT8, 28.2% identity
730 4q14 - Diatom allantoin synthase provides structural insights into natural fusion protein therapeutics 2018 J Oh, A Liuzzi, L Ronda, M Marchetti- ACS chemical, 2018 - ACS Publications Diatom Allantoin Synthase Provides Structural Insights into Natural Fusion Protein Therapeutics The 1.85--resolution crystal structure of allantoin synthase from the diatom Phaeodactylum tricornutum provides a rationale for the domain combinations observed in the metabolic The 1.85-Å-resolution structure of PtAlls was determined by molecular replacement program in PHENIX(55) by using the Urah structure from Brucella melitensis (PDB ID: 4Q14) as a search model.
731 5deo - Novel antimycobacterial compounds suppress NAD biogenesis by targeting a unique pocket of NaMN adenylyltransferase 2019 AL Osterman, I Rodionova, X Li, E Sergienko- ACS chemical, 2019 - ACS Publications ADVERTISEMENT. Log In Register. Cart. ACS; ACS Publications; C&EN; CAS. ACS Publications: ACS Journals; ACS eBooks; C&EN Global Enterprise. A; Accounts of Chemical Research; ACS Applied Bio Materials; ACS Applied Electronic
732 5udf - Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria 2021 I Alav, J Kobylka, MS Kuth, KM Pos, M Picard- Chemical, 2021 - ACS Publications Journal Logo. Structure , Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Ilyas Alav Ilyas Alav. Institute of Microbiology and Infection, College of Medical and Dental Sciences
733 4f47 - Post-translational Succinylation of Mycobacterium tuberculosis Enoyl-CoA Hydratase EchA19 Slows Catalytic Hydration of Cholesterol Catabolite 3-Oxo-chol-4,22 2020 AC Bonds, T Yuan, JM Werman, J Jang- ACS Infectious, 2020 - ACS Publications Cholesterol is a major carbon source for Mycobacterium tuberculosis (Mtb) during infection, and cholesterol utilization plays a significant role in persistence and virulence within host macrophages...
734 5vir 4ymi, 4fry Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target 2020 KH Burley, BJ Cuthbert, P Basu- ACS Infectious, 2020 - ACS Publications \ Interestingly, the three top-scoring NADP+ molecules are found in structures of Mtb nicotinamide-mononucleotide adenylyltransferase (NadD) (PDB ID: 4S1O) and Mycobacterium abscessus NadD (PDB ID: 4YMI and 5VIR). These results
735 4kzp - Enzymatic -Oxidation of the Cholesterol Side Chain in Mycobacterium tuberculosis Bifurcates Stereospecifically at Hydration of 3-Oxo-cholest-4,22-dien-24-oyl-CoA 2021 T Yuan, JM Werman, X Yin, M Yang- ACS Infectious, 2021 - ACS Publications The unique ability of Mycobacterium tuberculosis (Mtb) to utilize host lipids such as cholesterol for survival, persistence, and virulence has made the metabolic pathway of cholesterol an area of great interest for therapeutics development. Herein, we identify and characterize two genes from the Cho-region (... A search model for the apo-protein was created from 4KZP and the holo-protein model was created from the ChsB1 apo-protein model.
736 4wkw - Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis 2018 A Negri, P Javidnia, R Mu, X Zhang- ACS infectious, 2018 - ACS Publications Compared with published crystal structures of Rv2466c (PDB ID: 4NXI, 4ZIL) and the M. leprae homologue (PDB ID: 4WKW), there were significant conformational changes in one subunit of our structure
737 4k73 - Structural Basis for the Interaction and Processing of -Lactam Antibiotics by l,d-Transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis 2019 GA Libreros-Ziga, C dos Santos Silva- ACS Infectious, 2019 - ACS Publications Structural Basis for the Interaction and Processing of -Lactam Antibiotics by l,d-Transpeptidase 3 These structures revealed a fold and catalytic diad similar to those of other Ldts Mt The Ldt Mt3 faropenem structure indicated that faropenem is degraded after Cys-246 acylation The phases were obtained by molecular replacement with Phaser53 from CCP4 suite,54 adopting the PDB entries 4K73 and 5DU727 as models for LdtMt3 and LdtMt5 structures, respectively
738 5umh - Estimating Change in Foldability Due to Multipoint Deletions in Protein Structures 2020 A Banerjee, A Kumar, KK Ghosh- Journal of Chemical, 2020 - ACS Publications Figure S6: Root mean-square fluctuation of each residue of the protein in its original conformation (in magenta) and of the protein subject to MPD in residue stretches in the nonloop region (in sea green) for PDB IDs: 4XGQ chain A, 5UMH chain A, 4A5M chain A, 3GUD chain A, and...
739 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...
740 4nbr - PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations 2021 F Adasme-Carreno, J Caballero- Journal of Chemical, 2021 - ACS Publications Inf. Model. 2021, 61, 4, 1789-1800. ADVERTISEMENT. RETURN TO ISSUEPREVComputational Chemis...Computational ChemistryNEXT. Journal Logo. PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations
741 4hvt 5tnx, 3s6m SPOT-peptide: Template-based prediction of peptide-binding proteins and peptide-binding sites 2019 T Litfin, Y Yang, Y Zhou- Journal of chemical information and, 2019 - ACS Publications test set taken from another structure -based peptide-binding site predictor, SPRINT- peptide11 Structural genomics targets (SG4444) 11,813 proteins involved in structural genomics studies were collected from the PDB plate primarily based on domain-level structural similarity
742 6d6j 3oj7 Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc (II)-Binding Residues in Sites with Four Protein Ligands 2019 M Macchiagodena, M Pagliai, C Andreini- Journal of chemical, 2019 - ACS Publications quantum mechanical calculations on a training set of high-quality protein structures , encompassing the in the catalytic reaction of enzymes, by stabilizing the tertiary/quaternary structure of a cells.(5,7) The high thermodynamic stability of the tetrahedral zinc(II) structural sites in
743 6wpt - Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane 2021 YK Choi, Y Cao, M Frank, H Woo, SJ Park- Journal of chemical, 2021 - ACS Publications The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2) and is considered the major target for drug and vaccine development. We previously built fully glycosylated full-length SARS-CoV-2 S protein models in a viral membrane ... In the cryo-EM structure of the S trimer in the complex with the S309 antibody (PDB ids: 6WPS and 6WPT(51)), S309 interacts with the glycan attached to N343.
744 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...
745 4g50 3uqb Targeting Protein Folding: A Novel Approach for the Treatment of Pathogenic Bacteria 2020 NJ Scheuplein, NM Bzdyl, EA Kibble- Journal of Medicinal, 2020 - ACS Publications Infectious diseases are a major cause of morbidity and mortality worldwide, exacerbated by increasing antibiotic resistance in many bacterial species. The development of drugs with new modes of act...
746 5upg - Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity 2020 Y Yamada, H Takashima, DL Walmsley- Journal of Medicinal, 2020 - ACS Publications UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is a zinc metalloenzyme that catalyzes the first committed step in the biosynthesis of Lipid A, an essential component of the cell envelope of Gr... Figure 3. Detail of the crystal structure (PDB code: 5UPG) of 1 (PF-5081090) binding to the active site of PaLpxC
747 5vwm - Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria 2019 JP Surivet, P Panchaud, JL Specklin- Journal of Medicinal, 2019 - ACS Publications UDP-3-O-((R)-3-hydroxymyristoyl)-N-glucosamine deacetylase (LpxC) is as an attractive target for the discovery and development of novel antibacterial drugs to address the critical medical need crea...
748 6vxx - Developing a fully glycosylated full-length SARS-CoV-2 spike protein model in a viral membrane 2020 H Woo, SJ Park, YK Choi, T Park- The Journal of, 2020 - ACS Publications This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-l...
749 6vxx - Structural impact of mutation D614G in SARS-CoV-2 spike protein: enhanced infectivity and therapeutic opportunity 2020 A Fernndez- ACS medicinal chemistry letters, 2020 - ACS Publications Figure 1. Structural and epistructural interactions at the S1/S2 interface in the spike protein of SARS-CoV-2. (a) Positioning of D614 in the S1 chain (magenta) relative to T859 in the S2 chain (blue) at the S1/S2 interface for the spike protein structure reported in PDB6VXX
750 4jv3 4f32 Semisynthesis and Biological Evaluation of Platencin Thioether Derivatives: Dual FabF and FabH Inhibitors against MRSA 2021 Y Li, X Weng, Y Deng, J Pan, S Zhu- ACS medicinal, 2021 - ACS Publications The discovery and clinical use of multitarget monotherapeutic antibiotics is regarded as a promising approach to reduce the development of antibiotic resistance. Platencin (PTN), a potent natural a... On the basis of the X-ray structures of PTN with ecFabF(C163Q), Burkholderia vietnamiensis FabF, and Brucella melitensis FabB (PDB IDs 3HO2, 4F32, and 4JV3, respectively) as well as that of platencin A1 with ecFabF-(C163Q) (PDB ID 3HO9), it is likely that these PTN derivatives may also interact with FabF or
751 6nb3 - Discovery of Small Molecule Entry Inhibitors Targeting the Fusion Peptide of SARS-CoV-2 Spike Protein 2021 X Hu, CZ Chen, M Xu, Z Hu, H Guo, Z Itkin- ACS Medicinal, 2021 - ACS Publications SARS-CoV-2 entry into host cells relies on the spike (S) protein binding to the human ACE2 receptor. In this study, we investigated the structural dynamics of the viral S protein at the fusion pept... Comparison of the FP binding pocket of the spike protein of SARS-CoV-2 (PDB 6XR8), SARS-CoV-1 (PDB 5WRG), and MERS (PDB 6NB3). The spike protein is rendered in ribbons with the FP colored in magenta and the HR1 domain in blue.
752 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.
753 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
754 6q09 - Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity 2020 Z Ma, ML Caldas Nogueira, DP Marchi-Salvador- ACS, 2020 - ACS Publications Journal Logo. Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity. Zhongxin Ma Zhongxin Ma. Burnett School of Biomedical
755 6x79 - Characterization of the SARS-CoV-2 S protein: biophysical, biochemical, structural, and antigenic analysis 2020 NG Herrera, NC Morano, A Celikgil, GI Georgiev- ACS, 2020 - ACS Publications need to produce large quantities of high-quality SARS-CoV-2 Spike (S) protein for use in both clinical and basic science settings. To address this need, we have evaluated the expression and purification of two previously reported S protein constructs in Expi293F and ExpiCHO-S cells... In nine structures that align well in this region (conformation 1: 6VXX, 6X29, 6X2C, 6X79, 6ZOX, 6ZOY, 6ZP0, 6ZP1, 6ZWV), the amino acid segment 621–640 was not modeled, presumably due to disorder
756 4q4l - Design and Synthesis of Near-Infrared Mechanically Interlocked Molecules for Specific Targeting of Mitochondria 2020 RS Das, PC Saha, N Sepay, A Mukherjee- Organic, 2020 - ACS Publications The entrapment of squaraine (SQ) within a molecular container to form rotaxane has been shown to improve the dye stability and the fluorescence proficiency inside the mitochondria. The macrocycle p... The molecular docking of MSQ with Cys exposed mitochondrial protein ATP synthase subunit beta 1 (PDB: 4Q4L), and other SH-exposed proteins showed interactions between the SH moieties and MSQ
757 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
758 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
759 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
760 4gnv - A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to -lactams in Pseudomonas 2018 LA Ho, JL Winogrodzki, AW Debowski- Chemical, 2018 - pubs.rsc.org Fig. 2 Crystal structure of BcNagZ bound to 2. (A) Electron density (sigma-A weighted difference map (mF o DF c ) contoured at 4) for 2 (green carbon atoms (B) BcNagZ active site bound to 2 (green carbon atoms) with the BcNagZ product complex PDB 4GNV superposed
761 4odj - Nucleoside-modified AdoMet analogues for differential methyltransferase targeting 2020 NV Cornelissen, F Michailidou, F Muttach- Chemical, 2020 - pubs.rsc.org 39 In addition, we tested the putative wildtype MAT from Cryptosporidium hominis (ChMAT) that had been crystallized by the Seattle Structural Genomics Center for Infectious Disease (SSGCID) but was otherwise ChMAT ( PDB : 4ODJ ) and hMAT2a ( PDB : 5A1G) have 59
762 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
763 4xgi - Rational engineering of Acinetobacter tandoii glutamate dehydrogenase for asymmetric synthesis of l-homoalanine through biocatalytic cascades 2021 L Wang, S Diao, Y Sun, S Jiang, Y Liu- Catalysis Science &, 2021 - pubs.rsc.org on the crystal structure of GluDH from Burkholderia thailandensis ( PDB ID: 4XGI , resolution: 2.0 ) in symbiosum ( PDB ID: 1AUP and 1BGV) and GluDH from Corynebacterium glutamicum ( PDB ID: 5IJZ amino acid may cause loss of the inherent stability of the hydration structure
764 6vxx 6vyb Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations 2021 K Akisawa, R Hatada, K Okuwaki, Y Mochizuki- RSC Advances, 2021 - pubs.rsc.org Here, we report on interaction analyses of the spike protein in both closed ( PDB -ID: 6VXX ) and open interaction energies were evaluated for both structures , and a mutual comparison indicated considerable losses of stabilization energies in the open structure , especially in
765 4k9d - Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora 2021 AM Perez, JA Wolfe, JT Schermerhorn, Y Qian- RSC Advances, 2021 - pubs.rsc.org The PDB validation server shows this structure to be typical of structures of comparable resolution in measures of R and number of Ramachandran, sidechain and real-space R-value Z score (RSRZ) outliers ( PDB ID 6PX2) The model used for molecular replacement was 4K9D
766 6wps 7jvc, 7jva, 7jv6, 7jx3, 7k45, 7jw0 Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies 2021 J Chen, K Gao, R Wang, GW Wei- Chemical science, 2021 - pubs.rsc.org Our predictions are built from the X-ray crystal structure of SARS-CoV-2 S protein and ACE2 ( PDB 6M0J), 57 and various antibodies (PDBs 6WPS , 66 6XC2, 58 6XC3, 58 6XC4, 58 6XC7, 58 6XE1, 64 6XEY, 83 6XKP, 72 6XKQ, 72.
767 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
768 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
769 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
770 4ix8 - Caracterizacin estructural y funcional de la tirosina aminotransferasa de leishmania infantum 2016 M Moreno Izquierdo - 2016 - repositorio.uam.es ... Consequently the PLP-bonded structure of this enzyme was solved by X-raycrystallography at 2.35 of resolution. A comprehensive basis for the mechanismof the transamination in the active center allowed a structure-based ...
771 6tys - Planejamento de protenas imunognicas multi-eptopo visando o desenvolvimento de uma vacina de nova gerao para a infeco do vrus Nipah 2020 JMP GALCIO - 2020 - repositorio.ufopa.edu.br -defensin adjuvants were also added to the structural models to increase immunogenicity The interactions between each predicted epitope and MHC-I and MHC- II structures were also analyzed, using molecular modeling P Fosfoprotena PDB Protein Data Bank
772 5u29 - Sntese, elucidao estrutural e estudos in silico de novos compostos 2-amino-tiofnicos imdicos candidatos a frmacos antifngicos, antileishmanicida e 2019 ALC Pereira - 2019 - repositorio.ufpb.br Synthesis, structural elucidation and in silico studies of novel 2-amino- thiopheneic compounds imidic hybrids were synthesized with determined physicochemical characteristics and confirmed structures through 1H CYP51A1 ( PDB id: 1EA1); (B): ESBT-06 e FTAs ( PDB id: 3SFX
773 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 ...
774 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)).. ...
775 4wxt 5uth Mecanismo de ao e infeco por Corynebacterium pseudotuberculosis: expresso, purificao e caracterizao de protenas relacionadas ao metabolismo central 2017 LA Kawai - 2017 - repositorio.unesp.br Page 9. PBS: Tampo fosfato contendo NaCl PDB : Protein Data Bank RMN: Ressonncia Magntica Nuclear Corynebacterium pseudotuberculosis: Role of Electrostatic Forces in the Stability of the Secondary Structure , minha contribuio foi realizada na reviso final, onde
776 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
777 4k73 - L, D-transpeptidases de Mycobacterium tuberculosis: estudo das interaes com antibiticos -lactmicos e triagem de fragmentos 2018 GA Libreros-Ziga - 2018 - repositorio.unesp.br structure of LdtMt3 and its interactions with -lactam antibiotics, as well as the PDB Banco de dados de protenas (Protein Data Bank) Structural basis for the interaction and processing of -lactam antibiotics by L,D- transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis
778 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
779 4tyz - PROTEIN-PROTEIN INTERACTIONS OF HUMAN PARVOVIRUS B19 NS1 AND IDENTIFICATION OF THE NS1 TRANSCRIPTIONAL TRANSACTIVATION DOMAIN 2018 AL Morano - 2018 - repository.arizona.edu Page 1. PROTEIN-PROTEIN INTERACTIONS OF HUMAN PARVOVIRUS B19 NS1 AND IDENTIFICATION OF THE NS1 TRANSCRIPTIONAL TRANSACTIVATION DOMAIN Structure: Residues 112-214 share 32% sequence identity to x-ray crysal structure in PDB file 4TYZ chain A (a protein of unknown function).
780 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
781 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 ...
782 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).
783 4k6f - Cloning, expression and molecular modeling of the anthocyanidin reductase (FaANR) gene during strawberry fruit development 2017 PC Mandave, AA Kuvalekar, NL Mantri, MA Islam - 2017 - repository.up.ac.za on 3D structure of ANR obtained from homology modeling technique to check binding interaction of template molecule ( PDB ID: 4K6F ) with bound Their complex structure limits the com- mercial chemical synthesis and we are therefore highly re- liant on plants, especially
784 5dd7 - Structural and functional analysis of thiaminephosphate and homoserine kinases from Mycobacterium tuberculosis 2016 CM Ntui - 2016 - repository.up.ac.za Figure 3.17 X-ray diffraction pattern obtained from ThiL crystal Figure 3.18 The overall structure of MtbThiL Figure 3.20 Crystals obtained from optimization with ThrB Figure 4.1 Structural topology of MtbThiL with other ThiL structures PDB Protein Data Base pI Isoelectric point
785 5dd7 - Structural and inhibition studies of thiamine monosphosphate kinase from Mycobacterium tuberculosis 2020 LS Dlamini - 2020 - repository.up.ac.za OT Oxythiamine PDB Protein data bank 38 Figure 3.5: Crystal structure of MtbThiL homodimer ..... 40 bind to both free enzyme and the ES complex. Detailed structural information particularly high resolution crystal structures of substrate
786 4q14 - HISTIDINE PROTONATION AS A POSSIBLE MECHANISM FOR HUMAN TRANSTHYRETIN AMYLOIDOSIS: MODELLED AGAINST WALLABY 2020 DG D'SOUZA - 2020 - researchrepository.rmit.edu.au 0.97 indicated a highly conserved overall structure between the solved structure of wallaby TTR and a known crystal structure of human TTR ( PDB : 3U2I). The structural homology was strong with an almost perfect overlap of their peptide backbones, secondary, tertiary and ... Table 3.3 Predicted model of human TTR compared to other structurally similar proteins 7 4Q14 Brucella 0.806 1.62 0.283 0.890
787 4jpd - Dinmica molecular y consolidacin estructural de la frataxina humana 2016 SE Faraj - 2016 - ri.conicet.gov.ar The Alteration of the C-terminal Region of Human Frataxin Distorts its Structural Dynamics and Function Abajo: estructura de las protenas NB7804A de Bacillus halodurans ( PDB ID: 2KL4, amarillo); CyaY de Burkholderia cenocepacia ( PDB ID: 4JPD , gris), CyaY de
788 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. ...
789 4e98 4iyq Bases estructurales de la sealizacin y regulacin por nitrgeno y procesos asociados. 2019 L Tremio Agull - 2020 - riunet.upv.es PDB : banco de datos de protenas (Protein Data Bank: https://www.rcsb.org/ pdb /home/home. do) PEG 49 Captulo 1: Studies on cyanobacterial protein PipY shed light on structure , potential functions Functional and structural studies in bacteria ----- 117
790 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.
791 4lc3 - Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in Streptococcus pneumoniae 2018 X Han, R Sun, T Sandalova, A Achour- Open biology, 2018 - royalsocietypublishing.org The crystal structures of Spr1654 and in complex with PLP and PMP can direct the future rational design of novel therapeutic compounds against S. pneumoniae... The crystal structures were determined by molecular replacement in Phaser [40] using the crystal structure of UDP-4-amino-4-deoxy-l-arabinose-oxoglutarate aminotransferase from Burkholderia cenocepacia (PDB code: 4LC3) as search model.
792 4jgb 4jga TAK1: a potent tumour necrosis factor inhibitor for the treatment of inflammatory diseases 2020 J Totzke, SA Scarneo, KW Yang- Open, 2020 - royalsocietypublishing.org A general core structure for type II binders has been developed, consisting of a hydrophobic moiety Structural disorder of this region is often cited as a reason for the missing residues of Ligand 10 (purple, PDB 4JGA), 11 (orange, PDB 4JGB ) and 12 (dark green, PDB 4JGD) are
793 5bt8 - Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea 2020 M Rojas-Pirela, D Andrade-Alvirez- Open, 2020 - royalsocietypublishing.org bacteria, PGK, monomer, open, , 6I06, [39]. Acinetobacter baumannii, bacteria, PGK, monomer, , , 5BT8 , Fairman et al. (NA) Figure 3. Three-dimensional structure of phosphoglycerate kinase. (a) Ribbon representation of the overall structure of pig muscle PGK ( PDB : 1HDI)
794 4wgj 4xi8, 4py3, 4lu4 Fic and non-Fic AMPylases: protein AMPylation in metazoans 2021 BK Chatterjee, MC Truttmann- Open Biology, 2021 - royalsocietypublishing.org name, organism name, references, function/targets, structure ( PDB ID) BepC, Bartonella henselae, [59], triggers actin stress fibre formation in HeLa cells, 4WGJ salt bridges occur between (a) Asp117 and Lys119 of the extended flap region (a -hairpin like structure that partially
795 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
796 6nb8 - Drug Targets for Corona Virus (COVID-19): A Systematic Review 2020 K Jayakumar - 2020 - saudijournals.com to neutralize it, and their structures are also available ( PDB IDs: 6NB6, 6NB7, and 6NB8 .The monoclonal antibody, m396, has a competitive role for RBD binding ( PDB ID: 2DD8 However, the structure is highly variable among different members of the CoV family
797 5umh - Structural and Functional Studies of Proteins from the Agricultural Pests Tetranychus Urticae and Aspergillus Fumigatus 2017 C Schlachter - 2017 - scholarcommons.sc.edu Structural homologs of TuDioxygenase identified by the Dali server [51] were dioxygenases such as: SACTE_2871 (PDB code 4ILT, 153/155 residues aligned, RMSD 1.8 Å); catechol 1,2-dioxygenase from Burkholderia multivorans (PDB code 5UMH, 167/307 residues aligned
798 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
799 4j5i - Structural Studies in Natural Product Biosynthesis and Structure Determination 2016 L Han - 2016 - scholarship.rice.edu Page 1. Page 2. ABSTRACT Structural Studies In Natural Product Biosynthesis And Structure Determination by Lu Han Natural living organisms produce many natural compounds with diverse structures . They are one of the most productive sources of drug/bio-probe ... Taurine dioxygenase TauD from Mycobacterium smegmatis, Z= 17.5, r.m.s.d. 3.0Å over aligned Cα residues, id 15% (PDB 4J5I) (Baugh et al., 2015).
800 5b8f 3i3f, 3qxz Analysis of Pseudo-Symmetry in Protein Oligomers and its Correlation with Protein Dynamics 2017 K Shankar - 2017 - scholarworks.iupui.edu ... In fig.5.1, the protein with pdb code 1e9g is used to illustrate the structures generated to achievethe calculation. ... Fig. 5.2.: Structure Index in dimer 1e9g: Structural alignment of chain A with chainB generates A and chain B with A generates B. The difference between newly ...
801 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
802 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 ...
803 5eo6 - A molecular, structural, and cellular multiple-level study aimed at understanding the unique reaction catalyzed by the last enzyme in the heme-biosynthesis pathway of 2018 AI Celis Luna - 2018 - scholarworks.montana.edu Overlay of the structures of a representative heme b-bound chlorite dismutase and solvent This research aimed to understand ChdC function at the molecular, structural , and cellular levels The coproheme-bound ChdC structure revealed a helical-loop that is flexible and moves
804 4j3g - PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS 2019 B Strauss - 2019 - scholarworks.sjsu.edu set. Validated residue binary assignments of 0 (no change in secondary structure ) and 1 (change in secondary structure ) were determined (DSSP) from 3D X-ray structures for sets of virtually identical chains crystallized under different conditions
805 6q04 - Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate 2020 S Bangaru, G Ozorowski, HL Turner- , 2020 - science.sciencemag.org Report. Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate 1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
806 6ws6 - Insights into Innate Immune Response Against SARS-CoV-2 Infection 2021 A Huanu, AM Georgescu, AV Andrejkovits- Revista Romn de, 2021 - sciendo.com The NET structure made by activated neutrophils and mediated by reactive oxygen species bacterial lipopolysaccharides (LPS), flagella, cilia, bacterial unmethylated DNA, or viral structures like dsARN or In addition, sev- eral structural and non- structural SARS-CoV-2 proteins
807 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
808 5vog - ALIXE: a phase-combination tool for fragment-based molecular replacement 2020 C Milln, E Jimnez, A Schuster- Section D: Structural, 2020 - scripts.iucr.org 2.4.1. Hypothetical protein ( PDB entry 5vog ). The crystal structure of a hypothetical protein from Neisseria gonorrhoeae with bound ppGpp was downloaded from the PDB ( PDB entry 5vog ; Seattle Structural Genomics Center for Infectious Disease, unpublished work)
809 4eo9 - Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE 2018 DJ Rigden, JMH Thomas, F Simkovic- Section D: Structural, 2018 - scripts.iucr.org 1e59) was determined at a very high resolution (1.3 A ) while the other ( PDB entry 4eo9 ) was only at moderate resolution (2.45A). From this set, the structure of ecdysone phosphate phosphatase ( PDB entry 3c7t The third was a set of manually edited crystal structure derivatives
810 5bnt - Structure of aspartate -semialdehyde dehydrogenase from Francisella tularensis 2018 NJ Mank, S Pote, KA Majorek, AK Arnette- Section F: Structural, 2018 - scripts.iucr.org entry 3pzr; Pavlovsky et al., 2012), Pseudomonas aeruginosa ( PDB entry 5bnt ; Seattle Structural N-acetyl- -glutamyl-phosphate reductases (ArgCs), including proteins with known structure : ArgCs from entry 2i3a; Cherney et al., 2007), Salmonella typhi- murium ( PDB entry 2g17
811 4wbs - The structure of lipopolysaccharide transport protein B (LptB) from Burkholderia pseudomallei 2019 G Pankov, A Dawson, WN Hunter- Section F: Structural Biology, 2019 - scripts.iucr.org A single polypeptide from Paraburkholderia phymatum LptB ( PDB entry 4wbs ; Seattle Structural Genomics Center 2. The LptB subunit fold is conserved and displays no major conformational differences irrespective of whether the cofactor is present in the structure or not
812 5dld - Structural characterization of a nonhydrolyzing UDP-GlcNAc 2-epimerase from Neisseria meningitidis serogroup A 2020 NK Hurlburt, J Guan, H Ong, H Yu, X Chen- Section F: Structural, 2020 - scripts.iucr.org The 9 9 loop in NmSacA also contains a 310-helix, which is not observed in the E. coli structure . The structures of other epimerases with ligands bound in the active site, including those from Burkholderia vietnam- iensis ( PDB entry 5dld ; 48.7% identity; Seattle Structural
813 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
814 4f82 - Crystal structure of peroxiredoxin 3 from Vibrio vulnificus and its implications for scavenging peroxides and nitric oxide 2018 J Ahn, KK Jang, I Jo, H Nurhasni, GJ Lim, JW Yoo- IUCrJ, 2018 - scripts.iucr.org The structure of reduced Prx3 (C48D/C73S) was determined using the molecular-replacement method with MOLREP in the CCP4 package (Winn et al., 2011) using a putative thioredoxin reductase from Burkholderia ceno- cepacia ( PDB entry 4f82 ; Seattle Structural
815 5idv - Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization 2018 I Josts, S Niebling, Y Gao, M Levantino, H Tidow- IUCrJ, 2018 - scripts.iucr.org A total of 30 independent DAMMIF (Franke & Svergun, 2009) runs were performed to generate the initial structure pool (fit not shown). Calculated difference curves between the crystallographic dimer and monomer ( PDB codes 3b60 and 5idv ) show features similar to
816 6c9e 5vpr Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases 2020 JA Dunkle, MR Bruno, PA Frantom- Section D: Structural Biology, 2020 - scripts.iucr.org Q5ZXX6 6c9e , A L. pneumophila Lpg0604 Resting state Page 7 Six sequences/ structures belong to the IPR010970 SufS family by sequence homology, and inspection of these structures reveals that five possess the -hairpin structure and one, PDB entry 5vpr from
817 4odj - Structure of a critical metabolic enzyme: S-adenosylmethionine synthetase from Cryptosporidium parvum 2019 J Ohren, GF Parungao, RE Viola- Section F: Structural Biology, 2019 - scripts.iucr.org Vagin & Teplyakov, 2010) with the structure of C. hominus MetK ( PDB entry 4odj ) as the ordered in the presence of substrates, is disordered and was not modeled in this structure to form functional tetramers with D2 or 222 symmetry, as illustrated by EcoMetK ( PDB entry 1p7l
818 4f2n - Crystal structure of an iron superoxide dismutase from the pathogenic amoeba Acanthamoeba castellanii 2019 O Dao, K Asaithambi, BK Na, KH Lee- Section F: Structural Biology, 2019 - scripts.iucr.org et al., 2014), P. falciparum ( PDB entry 2bpi; Boucher et al., 2006) and L. major ( PDB entry 4f2n ; Phan et al., 2015) and of MnSOD from Homo sapiens ( PDB entry 5vf9 architecture of AcFeSOD is similar to those of other Fe/MnSODs, including the E. coli FeSOD structure (Fig
819 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
820 5ve7 - Crystal structure of UDP-glucose pyrophosphorylase from Yersinia pestis, a potential therapeutic target against plague 2019 ME Gibbs, GT Lountos, R Gumpena- Section F: Structural, 2019 - scripts.iucr.org A over 278 aligned residues, 72% sequence identity), Burkholderia ambifaria ( PDB entry 5ve7 ; rmsd of 1.3 A over 275 aligned residues, 52% sequence identity), Helico- bacter pylori ( PDB entry 3juk Figure 1 (a) Stereoview of a cartoon representation of the crystal structure of Y
821 6c87 6byq SIMBAD: a sequence-independent molecular-replacement pipeline 2018 AJ Simpkin, F Simkovic, JMH Thomas- Section D: Structural, 2018 - scripts.iucr.org researchers involved. All cases involve the crystallization of a known contaminant. Examples involving the use of SIMBAD for novel structure solution are available elsewhere, such as PDB entries 6byq, 6c87 and 5wol. Cases illustrating
822 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
823 4qhq - Structural insights into the substrate specificity of SP_0149, the substrate-binding protein of a methionine ABC transporter from Streptococcus pneumoniae 2019 B Jha, R Vyas, J Bhushan, D Sehgal- Section F: Structural, 2019 - scripts.iucr.org Z-score Rmsd (A ) Nalign %seq} Bound substrate PDB code Protein name and description 15.2 1.36 223 41 Met 4qhq A nutrient-binding protein (bound to methionine in the Sequence identity in SSM is calculated from structure (three-dimensional), rather than sequence
824 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
825 4iv5 - Theory, Design and Characterization of Protein Symmetry Combination Materials 2020 J Laniado - 2020 - search.proquest.com The symmetry group of a structure can be used to understand how many structurally distinct contact types are required to hold all the Current Opinion in Structural Biology 2016, 39:134143 built into a protein building block in order for it to assemble into the desired architecture
826 5ig2 3tjr Structural Genomics of Infectious Agents 2021 JS Alenazi - 2021 - search.proquest.com 4 1.3.5 Deposition of Structure in PDB ..... 4 identity to SDR from B.phymatum ( 5ig2 ) .... 45 S.3.2 Targeted approach of structure genomics can be applied to select the biologically important proteins
827 5upg - Widening the Therapeutic Window: Time-Dependent Inhibitors of LpxC and InhA for Treating Multidrug-Resistant Bacterial Infections 2018 C Gu - 2018 - search.proquest.com 46 Figure 2.10. X-ray crystal structure of paLpxC in complex with PF5081090 ( 5UPG . pdb ). ... 48 PD Pharmacodynamics PDB Protein Data Bank PIPES Piperazine-N,N-bis(2-ethanesulfonic acid) Sfp Phosphopantetheinyl transferase SKR Structure -kinetic relationship
828 6c87 6dbb, 6nab, 6byq Exploring Unconventional Approaches to Molecular Replacement in X-ray Crystallography with SIMBAD 2020 AJ Simpkin - 2020 - search.proquest.com to finding search models for MR is to use the sequence of the target structure to identify a approach is based on the assumption that sequence similarity is a useful guide to structural similarity final step is a brute-force search of a non-redundant derivative of the PDB provided by
829 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
830 5j92 - Preferential catabolism of the (S)enantiomer of the herbicide napropamide mediated by the enantioselective amidohydrolase SnaH and the dioxygenase Snpd in 2019 J Huang, D Chen, J Jiang- Environmental microbiology, 2019 - Wiley Online Library molecular docking. A homology model of Snpd was built based on chain A of the 5J92 template (sharing 39% identity with Snpd; PDB code; resolution: 1.95 ). A Snpd- KG-FeO complex structure was established in a similar manner as SnaH-Zn-H2O. The
831 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. ...
832 4f82 - Crystal Structures and Reaction Mechanism of 1-Cys Peroxiredoxin from Vibrio vulnificus 2016 - 2016 - s-space.snu.ac.kr ... 2011) using a putative thioredoxin reductase from Burkholderia cenocepacia ( PDB code 4F82 ) as a search model. ... proteins. A. The dimeric unit of the VvPrx3 (C48D/C73S) structure at the reduced ... tuberculosis (green; PDB code 1XXU). ...
833 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
834 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
835 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.
836 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
837 6mb1 6maz, 6may, 6mb0 N-myristoyltransferase inhibitor binding mode and phenotype in the malarial parasite. 2019 AC Schlott - 2019 - spiral.imperial.ac.uk lacks myristoylation and instead contains a hydro- phobic N-terminal sequence interacting with the Golgi membrane; its location resembles the distribution of GRASP1, but its structure may result 2010) N-Myristoyltransferase from Leishmania donovani: Structural and Functional ... One of them is the aminomethylindazole series including compounds IMP-0917 (PDB: 5O6H) (Mousnier et al. 2018), and IMP-1002 (PDB: 6MB1) (Schlott et al. 2019)
838 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 ...
839 4lsm 4k9d, 6ok4 Estudos estruturais das enzimas urocanato hidratase de Trypanosoma cruzi, gliceraldedo-3-fosfato desidrogenase de Schistosoma mansoni e glicose-6-fosfato-1 2020 S Boreiko - 2020 - tede2.uepg.br the conformation of monomers A and C, which were explored to understand structural changes in 1-Epimerase, also part of the glycolytic pathway, had its structure modeled by e Homo sapiens 2 (cdigo PDB 3H9E), Trypanosoma cruzi (cdigo PDB 4LSM ), Arabidopsis thaliana
840 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), ...
841 5vrb 3uk1, 3upt, 4xeu Ingnierie de la transctolase de Geobacillus stearothermophilus: nouvelles stratgies pour la synthse enzymatique de cetoses rares 2017 M Lorilliere - 2017 - tel.archives-ouvertes.fr Neisseria gonorrhoeae (2017) (5VRB.pdb) ou Chlamydomonas reinhardtii (2017) [76], toutes les TKs sont dimériques et constituées de deux sous-unités
842 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
843 4qhq - Dveloppement d'un alphabet structural intgrant la flexibilit des structures protiques 2018 I Sekhi - 2018 - tel.archives-ouvertes.fr 84 4.2.2 Architecture du site web 2.5 Comparaison de temps d'excution de SAFlex- PDB avant et aprs optimisation ensemble de conformations gomtriques reprsentatif des fragments protiques, appels lettres structurales (LS) , et destines simplifier la structure 3D d
844 4e51 - Incorporation de la beta alanine dans des polypeptides 2019 G Nigro - 2019 - tel.archives-ouvertes.fr 89 I. 2 Structures de la MetRS cocristallise avec des analogues de la mthionine : Sites de reconnaissance des acides aminés de trois AARS de classe II. A : HisRS de Burkholderia thailandensis (4E51), B :
845 4qhq - Structural and Functional Characterization of the Escherichia coli MetNI Methionine Transporter 2018 PT Nguyen - 2018 - thesis.library.caltech.edu PTN participated in soaking experiments for the L-semethionine-bound MetNI structure ( PDB :3TUZ) and manuscript preparation. Page 12. xii transporter architecture and mechanism. Science 16. Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J. Crystal structure of a
846 4xgi - Engineering, Predicting, and Understanding Nicotinamide Cofactor Specificity 2016 JKB Cahn - 2016 - thesis.library.caltech.edu geometries between homologues,11,12 and this structural diversity has limited the development of general methods PDB accession code use the cofactor from that protein and (m) denotes a structure of a mutant protein
847 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
848 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 ...
849 4lfy - STRUCTURE DETERMINATION AND BIOCHEMICAL CHARACTERIZATION OF NOVEL HUMAN UBIQUITIN-LIKE DOMAINS. 2015 RS Doherty - 2015 - tspace.library.utoronto.ca ... Table 3.2: Secondary structure elements of NFATc2IP, ubiquilin-1, ubiquitin and SUMO1/2/3. ...Table 3.4: UIM:ubiquitin complexes deposited in the PDB, along with UIM sequence ... ubiquitin,along with the number of supporting publications and supporting structural complexes that ...
850 6cw5 - In silico Structural Modelling of Ribokinase from Salmonella Typhi 2021 H Abubakar, Y Ndatsu, AD Musa, C Ogbiko- Earthline Journal of, 2021 - ubipayroll.com done to check the stereochemical features of the predicted 3-dimensional structure of the BLASTp showed low identity of 40% (Table 1) with other proteins deposited in PDB and conserved domain (Figure 1). Multiple sequence alignment between the query, 6CW5 , 2FV7, 1VM7
851 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
852 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)
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