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 5EO6 - 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..
2 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 ...
3 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 E. Ahmed & S. Gourinath, unpublished work) and Mycobacterium ulcerans Agy99 (PDB entries 3qi6 and 3qhx ...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. ...
4 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 ...
5 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.. ...
6 3iml 3dms, 3hja, 3gtd, 3mbf, 3sth, 3s82, 3qbp, 3l0d, 3kx6, 4oh7, 4xfj, 4tu1 Investigation of intrinsic dynamics of enzymes involved in metabolic pathways using coarse-grained normal mode analysis 2017 SM Meeuwsen, AN Hodac, LM Adams - Cogent , 2017 - Taylor & Francis ... (3IML), and M. avium (3S82) MATs together. The dynamics of 3IML are more similar to the ... 6) toassist in the open and closed conformations of the enzyme. Ornithine transcarbamylase (PDBcode: 4OH7; chains A and B of the homotrimer were ... Visualization of the structure ...
7 3u0g - A Novel highly thermostable branched-chain amino acid aminotransferase from the crenarchaeon Vulcanisaeta moutnovskia 2017 TN Stekhanova, AL Rakitin, AV Mardanov - Enzyme and Microbial , 2017 - Elsevier ... The first X-ray diffraction structure of BCATs, namely, the structure of BCAT ... The search for close homologues of VMUT0738 using BLAST showed the highest levels of identity with hypothetical BCATs from other members of the genera Vulcanisaeta … The homologues with known structures were TUZN1299 from T. uzoniensis (PDB ID 5CE8, 54% identity, query cover 94%), putative BCAT from Burkholderia pseudomallei (PDB ID 3U0G, 47% identity, query cover 94% ...
8 4fur - Differential Antibody Responses to Conserved HIV-1 Neutralizing Epitopes in the Context of Multivalent Scaffolds and Native-Like gp140 Trimers 2017 CD Morris, P Azadnia, N de Val, N Vora, A Honda - mBio, 2017 - Am Soc Microbiol ... Following structural and antigenic evaluation, a subset of scaffold and trimer antigens was selected for immunization in BALB/c mice. Serum binding revealed distinct patterns of antibody responses to these two bNAb targets presented in different structural contexts. ... Reference-free 2D class averages of scaffolded gp140.681.R1 trimers containing TS domains 1NOG, 1V6H, 4FUR, 1TCZ, and 1VH8. ...
9 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 ...
10 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. ...
11 4ege - Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro 2017 VN Are, A Kumar, S Kumar, VD Goyal, B Ghosh - et Biophysica Acta (BBA , 2017 - Elsevier ... are lacking with literature reports of either only structural data (PDB entries; 1WN1, 1WY2, 3Q6D,2IW2, 4EGE) or only ... for this was prepared by Chainsaw [26] using the XPDxc protein sequenceand the structure of a putative XPD from Thermococcus sibiricus (PDB: 4FKC) [8 ...
12 4o5h - Structure and biochemistry of phenylacetaldehyde dehydrogenase from the Pseudomonas putida S12 styrene catabolic pathway 2017 AG Crabo, B Singh, T Nguyen, S Emami - Archives of Biochemistry , 2017 - Elsevier ... The closest structural homolog to NPADH is sheep liver aldehyde dehydrogenase ALDH1 (PDBID: 1BXS), which catalyzes the conversion of retinal to retinoic ... In a homologous PADH structure from Burkholderia cenocepacia J2315 (BcPADH) (PDB ID: 4O5H), which was recently solved by the Seattle Structural Genomics Consortium and has 49% identity and 65% similarity to PADH, this loop contains the same number of amino acids as NPADH and adopts a different orientation (Fig. 2C)...
13 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. ...
14 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 ...
15 4n0w 4m9a, 4m0j, 4oo0, 4o5o, 4o5m, 4oh7 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. ...
16 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),. ...
17 4wec - Binding of NADP+ triggers an open-to-closed transition in a mycobacterial FabG -ketoacyl-ACP reductase 2017 M Blaise, N Van Wyk, F Banres-Roquet - Biochemical , 2017 - biochemj.org ... A BLAST analysis using the MSMEG_6753 primary sequence to query the protein databank shows that the crystal structures of Ralstonia sp. alcohol dehydrogenase [24] (PDB:4BMS), Bacillus subtilis FabG [18] (PDB:4NBU) and the uncharacterized SDR MSMEG_2598 (PDB:4WEC) from M. smegmatis (unpublished) possess the highest scores, sharing 42, 37 and 37% primary sequence identity with MSMEG_6753, respectively ...
18 4jnq - Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation 2017 MS Setzer, KG Byler, IV Ogungbe, WN Setzer - Scientia Pharmaceutica, 2017 - mdpi.com ... Page 8. Sci. Pharm. 2017, 85, 5 8 Figure 4. Overlay of the protein structures of Brucella melitensisTxR, PDB 4JNQ [24] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blueribbon). The co-crystallized ligand is shown as a wireframe structure. ...
19 3v7o - Design of an expression system to enhance MBP-mediated crystallization 2017 T Jin, W Chuenchor, J Jiang, J Cheng, Y Li - Scientific , 2017 - ncbi.nlm.nih.gov ... 25 , GST 26 , TRX 27 , green fluorescent protein (GFP) 28 ,29 , SUMO (pdb: 3V7O and 4G50 ...platform is increasingly appreciated 38 ,39 , the optimal sequence, length, and structure of the ...The death domain superfamily is a structural motif found in many proteins that are involved ...
20 4tmd - Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis 2017 E Sviridova, P Rezacova, A Bondar, V Veverka - Scientific , 2017 - ncbi.nlm.nih.gov ... Structural similarity searches revealed that none of the deposited structures in the Protein DataBank ... Using the DALI server, the best fit was obtained for the crystal structure of the hypotheticalprotein MSMEI_5302 from Mycobacterium smegmatis (PDB: 4TMD), an Rv0999 ...
21 4o6r - Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway 2017 B Jia, X Jia, KH Kim, ZJ Pu, MS Kang, CO Jeon - Scientific Reports, 2017 - ncbi.nlm.nih.gov ... using the Modeller 9 program 28 based on the crystal structures of SALDpp (PDB ID: 4JZ6) andother aldehyde dehydrogenases (PDB ID: 4FR8, 4O6R, 4NMK, 2O2P, and ... The three-dimensionalstructure of SALDan was modeled using the Modeller 9 software program 28 . ...
22 4h3z 4odj How to fold intricately: using theory and experiments to unravel the properties of knotted proteins 2017 SE Jackson, A Suma, C Micheletti - Current Opinion in Structural Biology, 2017 - Elsevier ... Despite the early evidence of a shallowly knotted carbonic anhydrase structure [1 and 2], the ...Homodimeric entries 3BJX and 4H3Z are accordingly represented by chains B instead of thedefault ... The complete list of knotted PDB entries, including a few where knots are likely ...
23 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 ...
24 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%).. ...
25 3he2 - THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria 2016 JAG Cox, KA Abrahams, C Alemparte - Nature , 2016 - nature.com ... Using M. tuberculosis EchA6 (PDB entry 3HE2) as a search model, we determined initial phases by molecular replacement (PHASER39). The models were rebuilt and refined (COOT40, REFMAC541, PHENIX.REFINE42) using non-crystallographic symmetry ...
26 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). ...
27 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. ...
28 3k9w - Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa 2016 R Chatterjee, A Mondal, A Basu, S Datta - Biochimica et Biophysica Acta ( , 2016 - Elsevier ... 5-phosphosulfate [PDB ID: 3OTW, 3NV7] [29] and Burkholderia pseudomallei in complex withhydrolyzed dPCoA [PDB ID: 3K9W] [30]. ... was solved using PHASER [38] and by utilizing E. coliphosphopantetheine adenylyltransferase (1HIT chain A) as a starting structure. ...
29 3quv - Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase 2016 HN Im, HS Kim, DR An, JY Jang, J Kim, HJ Yoon - Journal of Structural , 2016 - Elsevier ... (ii) nucleic acid MTases [Rv2118c (PDB: 1I9G; Gupta et al., 2001), Rv2372c (PDB: 4L69; Kumar et al., 2014), Rv2966c (PDB: 3P9N; Sharma et al., 2015), and MAB_3226c (PDB: 3QUV)] ...
30 3gwc - An In Silico Approach for Identification of Potential Anti-Mycobacterial Targets of Vasicine and Related Chemical Compounds 2016 A Kashyap Chaliha, D Gogoi, P Chetia - chemistry & high , 2016 - ingentaconnect.com ... (Table 5). Chemical similarity search of vasicine using PubChem Structure Search yielded ... SlNo. PDB ID Protein Name Protein Name (Short) Gene Name Resolution (A ... 9 3FV5 E. coliTopoisomerase IV Topo IV b3030 1.80 10 3GWC Thymidylate synthase X ThyX Rv2754c 1.90 ...
31 2khp - An NMR-guided screening method for selective fragment docking and synthesis of a warhead inhibitor 2016 RB Khattri, DL Morris, CM Davis, SM Bilinovich - Molecules, 2016 - mdpi.com ... The active site architecture of BrmGRX matches with the proposed GRX consensus active sitestructure which suggests the N ... Structures of target proteins were obtained from the Protein DataBank (PDB) [63]. The PBD code for BrmGRX is 2KHP and hGRX1 is 1JHB [19,64]. ...
32 4ylg - Cryo-EM structure of the yeast U4/U6. U5 tri-snRNP at 3.7 resolution 2016 THD Nguyen, WP Galej, X Bai, C Oubridge - Nature, 2016 - nature.com ... 4: Secondary structure of the snRNAs in tri-snRNP. ... S. pombe ILS spliceosomal complex 19, 20(red, PDB 3JB9), was overlaid on GDPs found in other guanine-nucleotide binding proteins(grey, PDB coordinates: 1DAR, 2E1R, 2WRI, 1Z0I, 5CA8, 1XTQ, 4YLG, 1SF8, 5BXQ ...
33 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. ...
34 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 ...
35 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. ...
36 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) ...
37 4g50 4ggq Development, synthesis and structureactivity-relationships of inhibitors of the macrophage infectivity potentiator (Mip) proteins of Legionella pneumophila and 2016 F Seufert, M Kuhn, M Hein, M Weiwad, M Vivoli - Bioorganic & Medicinal , 2016 - Elsevier ... Structural comparison between BpMip and LpMip showed a high homology in the PPIase domain. ...A (left) and region B (right) of lead compound CJ168 (shown in orange in PDB structure 4G503 ). The ... In fact, from the BpMip crystal structures and the LpMip docking modes, the ...
38 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. ...
39 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 ...
40 3ek2 - Pyridone FabI Inhibitors and Uses Thereof 2016 P Tonge - US Patent App. 15/130,365, 2016 - Google Patents ... Selected residues of the saFabI-NADPH-PT173 structure (gray, subunit F) and the centralhydrogen ... Structural differences between diphenyl ether and pyridone ternary complexes. ... residueroot mean square deviation (RMSD) values between the triclosan-bound (PDB code 4ALI ...
41 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 ...
42 4gri 4g6z Interplay between Catalysts and Substrates for Activity of Class Ib Aminoacyl-tRNA Synthetases and Implications for Pharmacology 2016 P Stephen, SX Lin, R Gieg - Current topics in medicinal , 2016 - ingentaconnect.com ... Eukarya) and limited records for ArgRS (13 PDB entries) and LysRS-1 (1 PDB entry ... with that ofEcoGlnRS and dem- onstrated the presence of GluRS-specific secondary-structure insertions ...aaRS:small ligands Eco (4OBY) Bbu(4GRI) Bth(4G6Z) Tel (2CFO) Tma (3AFH) Tth (1J09 ...
43 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 ...
44 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 ...
45 3v2i - Small Molecule Docking Supports Broad and Narrow Spectrum Potential for the Inhibition of the Novel Antibiotic Target Bacterial Pth1 2016 PP Ferguson, WB Holloway, WN Setzer, H McFeeters - Antibiotics, 2016 - mdpi.com ... were obtained from the Protein Data Bank and each structure was analyzed for ... The Pth1 setincluded eight bacterial structures: Escherichia coli (PDB 2PTH) [11 ... aeruginosa (4FYJ) [14],Francisella tularensis (3NEA) [15], Burkholderia thailandensis (3V2I) [31], Acinetobacter ...
46 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 ...
47 3uw3 - Molecular Docking and Dynamics Simulation of Vibrio anguillarum Aspartate Semialdehyde Dehydrogenase with Natural Product Caulerpin 2016 P Aiya Subramani, R Mahendran - Letters in Drug , 2016 - ingentaconnect.com A MGGEYLSAFTVGDQLLWGAAEPLRRMLRILLDK ... 7). Further structuralchar- acterisation needs to be done ... middle is due to an unfavourable secondary loop structure. ...
48 3qi6 3qhx, 3ndn 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. ...
49 3oq8 - Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum 2016 Y Park, Y Cho, YH Lee, YW Lee, S Rhee - Journal of structural biology, 2016 - Elsevier ... The MoICL residues were selected based on the proposed structural and functional features ... In previous, unpublished work, we also observed nearly identical structural changes in Brucella melitensis ICL complexed with malonate (PDB 3OQ8). ...
50 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 ...
51 4h51 3meb, 4w5k 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, ...
52 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)) ...
53 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 ...
54 4qtp - Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets 2016 A Gazi, MG Kibria, M Mahfuz, R Islam, P Ghosh - Gene, 2016 - Elsevier ... Conformational B cell epitopes of NP_216420.1 (UniProt ID: O07728) predicted from the 3D structure template under PDB ID 4QTP (Crystal structure of an anti-sigma factor antagonist from M. paratuberculosis). ...
55 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 ...
56 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. ...
57 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 ...
58 3eoo - Design, Synthesis and Evaluation of Pyrazolo-Pyrazole Derivatives onMethylisocitratelyase Of Pseudomonas aeruginosa: Insilico and invitro study 2016 M Pulaganti, C Suresh Kumar - Journal of Biomolecular Structure , 2016 - Taylor & Francis ... possessing the highest sequence identity. We finally picked the A-chain of 1MUM and 3EOOas ... carefully editing PIR file and PDB file template.The developed .ali, .py, pdb template files ...structure of MICL with build command of modeller, using default parameters. ...
59 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. ...
60 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. ...
61 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 ...
62 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 ...
63 3s6d - Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei 2016 AA Lopez-Zavala, JS Carrasco-Miranda - et Biophysica Acta (BBA , 2016 - Elsevier ... Glycolysis is one of the most regulated metabolic pathways, however little is known about thestructural mechanisms for its regulation in non-model ... Using the DALI server [53] to look for similar structures, the root mean square deviation (RMSD) for backbone carbons between LvTIM and...P. falciparum (1WOB) 1.5 A, Coccidioides immitis (3S6D) 2.1 A
64 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. ...
65 3ek1 3i44 A computational integrating kinetic study on the flexible active site of human acetaldehyde dehydrogenase 1 2016 Y Xu, J Lee, HS Yang, ZR L, H Mu, JM Yang - Process , 2016 - Elsevier ... In the first step, binding pocket residues were calculated based on the 3D structure of ALDH1via the Pck pocket ... We found 25 template PDB structures (1a4s, 1bxs, 1euh, 1o04, 1t90, 1uxt,1uzb, 1wnd, 2d4e, 2imp, 2j6l, 2o2p, 2ve5, 2w8n, 3b4w, 3ed6, 3ek1, 3i44, 3ifg, 3jz4 ...
66 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 ...
67 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 ...
68 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 ...
69 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). ...
70 4dhe - Molecular dissection of the interface between the Type VI secretion TssM cytoplasmic domain and the TssG baseplate component 2016 L Logger, MS Aschtgen, M Gurin, E Cascales - Journal of Molecular , 2016 - Elsevier ... a C-terminal extension (Ct, green). TssM Cyto/NTP was modelled using HHpredbased on the X-ray structure of the Burkholderia thailandensis EngB GTP-bindingprotein (PDB ID: 4DHE). TssM Cyto/Ct was modelled using ...
71 3e7d - POLYPEPTIDES FOR USE IN SELF-ASSEMBLING PROTEIN NANOSTRUCTURES 2016 D Baker, JB Bale, NP King - US Patent , 2016 - freepatentsonline.com ... panel B) comprise 12 pentamers (dark grey) and 30 dimers (light grey), and the I32-28 designmodel and crystal structure (panel C ... Starting proteins were those derived from pentameric, trimeric,and dimeric crystal structures from the Protein Data Bank (PDB), along with a ...
72 4f36 4p8r, 4fkx, 4f4a, 4fky The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected DiseasesPart III: In-Silico Molecular Docking 2016 IV Ogungbe, WN Setzer - Molecules, 2016 - mdpi.com ... accessibilities: (1) in most cases the protein is modeled as a rigid structure without flexibility;(2 ... compounds that may themselves function as efficacious drugs, may serve as lead structuresfor chemical modification and optimization, or provide structural templates for de ...
73 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). ...
74 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) ...
75 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 ...
76 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). ...
77 3gaf - The three-dimensional structure of Clostridium absonum 7-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP (H) 2016 D Lou, B Wang, J Tan, L Zhu, X Cen, Q Ji - Scientific reports, 2016 - ncbi.nlm.nih.gov ... They are Brucella Melitensis 7-HSDH with no ligand (PDB code: 3GAF) at resolution 2.20 and Escherichia coli 7-HSDH (EC 7-HSDH; PDB code: 1FMC ... As one of the SDRs, with thesimilar structure to the two 7-HSDHs above, CA 7-HSDH possesses the ...
78 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. ...
79 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 ...
80 3nrr - Human Dihydrofolate Reductase and Thymidylate Synthase form a complex in vitro and co-localize in normal and cancer cells 2016 A Antosiewicz, A Jarmua, D Przybylska - Structure and , 2016 - Taylor & Francis ... (Konagurthu, Whissto Stuckey, & Lesk, 2006). The AB dimer of the human TS structure 1HVY(Phan et al., 2001) and monomer A of the DHFR structure 1KMS (Klon et al., 2002) ... PDB ID: 3NRR)(Begley et al., 2011), Cryptosporidium hominis (Ch; PDB ID: 1QZF) ...
81 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 ...
82 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 ...
83 3ixc - Molecular Docking Studies of Wolbachia Endosymbiont of Brugia Malayi's Carbonic Anhydrase Using Coumarin-chromene Derivatives Towards Designing Anti-filarial 2016 P Malathy, G Jagadeesan, K Gunasekaran - , 2016 - earticle.net ... The BLAST results shows a hexapeptide transferase family protein from Anaplasmaphagocytophilum (PDB ID: 3IXC) having 77% similarity and 54% identity with wBm carbonicanhydrase. Hence the above enzyme is chosen as the template and the 3D structure of carbonic ...
84 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. ...
85 2lol 2kwl, 2lky Dynamic Analysis of Backbone-Hydrogen-Bond Propensity for Protein Binding and Drug Design 2016 CA Menndez, SR Accordino - Biopolymers for , 2016 - crcnetbase.com ... binding (Bogan and Thorn 1998; Li and Liu 2009) propose that the structure of the ... layers of aset of complete (without missing residues) proteins without ligands (PDB IDs: 1AHO ... 2L4V, 2L5R,2L7W, 2LA1, 2LAO, 2LCU, 2LFN, 2LHC, 2LHS, 2LJM, 2LKB, 2LKY, 2LOL, 2LPK, 2PNE ...
86 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 ...
87 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 ...
88 3mmt - Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non- 2016 CM Carnielli, J Artier, JCF de Oliveira - Data in Brief, 2016 - Elsevier ... ID, Gene symbol, ENSEMBL, SWISS-PROT, Protein structure (PDB), Conserved domain (CDD),Gene ontology (GO). ... GO:0003735 structural constituent of ribosome, ... citri (strain 306) GN=XAC3344PE=3 SV=1, 3mmt Fructose-bisphosphate aldolase, cd00948, FBP_aldolase_I_a ...
89 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);. ...
90 3qh4 - Identification of amino acids related to catalytic function of Sulfolobus solfataricus P1 carboxylesterase by site-directed mutagenesis and molecular modeling 2016 YH Choi, YN Lee, YJ Park, SJ Yoon, HB Lee - BMB reports, 2016 - ncbi.nlm.nih.gov ... the basis of the Protein Data Bank (PDB) databases reported previously: AfuEst (PDB code: 1jji ...esterase (1qz3), MetEst (2c7b), StoEst (3aik), Mycobacterium marinum esterase (3qh4), PcaEst(3zwq ... was created by homology modeling as the superimposed ribbon structure onto it ...
91 3sbx - Structural basis for cytokinin production by LOG from Corynebacterium glutamicum 2016 H Seo, S Kim, HY Sagong, HF Son, KS Jin - Scientific , 2016 - ncbi.nlm.nih.gov ... also showed that LOGs from C. purpurea (CpLOG, PDB CODE 5AJT, Z-score 26.8) and M.marinum (MmLOG, PDB CODE 3SBX, Z-score ... To compare CgLOG with other LOGs, wesuperposed the CgLOG structure with other LOG proteins such as AtLOG3, CpLOG, and ...
92 4di0 - Aerobic lineage of the oxidative stress response protein rubrerythrin emerged in an ancient microaerobic,(hyper) thermophilic environment 2016 JP Cardenas, R Quatrini, DS Holmes - Frontiers in Microbiology, 2016 - ncbi.nlm.nih.gov ... F9VPE5; PDB entry 1J30) and a rubrerythrin from Burkholderia pseudomallei (Uniprot accessionQ3JK2; PDB entry 4DI0) have three dimensional structures in the PDB. ... This difference in genecluster structure among members of the same phylum may be a reflection of the ...
93 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 ...
94 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 ...
95 3tcq - Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40 2016 MU Mirza, N Ikram - International Journal of Molecular Sciences, 2016 - mdpi.com ... We have identified VP40 assemblies in a filamentous structure and have shown that disruption of these structures halts viral egress... The homology-based search inferred that the 3D coordinate crystal structure of the Reston Ebola virus RNA binding domain (PDB ID: 3KS4), in addition to the crystal structure of the Sudan Ebola virus matrix protein VP40 (PDB ID: 3TCQ), were the best hits based on query coverage ...
96 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) ...
97 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 ...
98 3nfw - Biochemical properties and crystal structure of the flavin reductase FerA from Paracoccus denitrificans 2016 V Sedlek, T Klumpler, J Marek, I Kuera - Microbiological Research, 2016 - Elsevier ...Sequence and structural comparisons of FerA with a flavin reductase like domain protein family (PF01613). 3NFW E5Q9D7 NmoB Mycobacterium thermoresistibile ...
99 3dmp - Unravelling the Potential of a New Uracil Phosphoribosyltransferase (UPRT) from Arabidopsis thaliana in Sensitizing HeLa Cells towards 5-Fluorouracil 2016 S Narayanan, P Sanpui, L Sahoo, SS Ghosh - International journal of , 2016 - Elsevier ... UPRT templates from Protein Data Bank (PDB) PDB: 2EHJ (E. coli UPRT), PDB: 3DMP(Burkholderia pseudomallei UPRT) and PDB: 1BD4 (Toxoplasma gondii UPRT) were chosenfor generating the three ... 1). The three-dimensional structure of AtUPRT ( Fig. ...
100 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). ...
101 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 ...
102 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. . ...
103 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 ...
104 4o3v 4kz1, 4lso, 4nhf VirB8-like protein TraH is crucial for DNA transfer in Enterococcus faecalis 2016 C Fercher, I Probst, V Kohler - Scientific , 2016 - ncbi.nlm.nih.gov ... A structure-based homology search revealed that TraH is related to proteins of the VirB8 family,which all exhibit a ... PDB code 4NHF, 14% sequence identity), Bartonella quintana (PDB code 4LSO,6% sequence identity), Rickettsia typhi (PDB code 4O3V, 19% sequence ...
105 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 ...
106 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.. ...
107 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. ...
108 4mow - Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase 2016 AM de las Heras - Microbial Cell , 2016 - microbialcellfactories.biomedcentral. ... Since the crystal structures of these AARs were not available, protein structures were made ... protein sequence identity to the C. necator AAR whose crystal structure was used ... Both S. wolfei homology models (Swol_0651 modelled on PDB: 4MOW [27] and Swol_1910 modelled ...
109 3rd5 - Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR) 2016 BRK Menon, SJO Hardman, NS Scrutton - of Photochemistry and , 2016 - Elsevier ... A putative uncharacterized SDR protein (PDB id: 3RD5) that has the highest sequence identitywith POR was used as the reference structure and the sieving procedure removed 68% of the3RD5 residues at 1.8 sieving level using Mustang-MR sieving server. ...
110 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 ...
111 2lwk - Recent Advances in Developing Small Molecules Targeting Nucleic Acid 2016 M Wang, Y Yu, C Liang, A Lu, G Zhang - International journal of molecular , 2016 - mdpi.com ... Figure 12A) consists of a planar ring, an amino sugar structure and a fused cyclohexane ringsystem. A lot of structural studies have been investigated to understand the interaction betweenDNA duplex and molecule [28,46,47,48,49,50,51]. Most of the structures indicate that ...
112 3dpi - Protein-protein interaction and molecular dynamics analysis for identification of novel inhibitors in Burkholderia cepacia GG4 2016 M Gupta, R Chauhan, Y Prasad, G Wadhwa - Biology and Chemistry, 2016 - Elsevier ... Homology based protein structure prediction employs submission of query protein sequenceto BLASTp against PDB database for identifying ... 3DPI, 2PZ8 and 1NSY. ... The dimensions of bindingspace on three dimensional structure of protein were identified in DockBlaster itself. ...
113 4qq7 - Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica 2016 H Do, IS Kim, BW Jeon, CW Lee, AK Park, AR Wi - Scientific Reports, 2016 - nature.com ... C with an RMSD of 2.07 ) and the putative stringent starvation protein A from Burkholderiacenocepacia (PDB code 4QQ7) (122 aligned C ... The dimer structure of CLIC1 has a largehydrophobic surface, which can be used for membrane incorporation and chloride ion ...
114 3p96 3k9g, 3km3 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 ...
115 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 ...
116 3rmi - A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment 2016 B Ekim - academia.edu ... Four uncharacterized proteins (1IVZ, 3B4Q, 3DDE, and 4RGI) and their closest structural neighbors (2E7V, 3RMI, 3HLX, and 5BV3, respectively), printed as output by Esperite (Cosine distance between any one of the pairs were 0.0), and to be investigated further through protein nuclear magnetic resonance spectroscopy. ...
117 3vab - Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis 2016 MG Peverelli, TPS da Costa, N Kirby - Journal of Biological , 2016 - ASBMB ... and 1TUF) (9), Aquifex aeolicus (PDB code 2P3E), and Brucella melitensis (PDB code 3VAB)show that ... both a dimer (PDB codes 1HKW and 1HKV) (7) and a tetramer (PDB code 2O0T ... arethe results of earlier studies aimed at characterizing the quaternary structure of DAPDC ...
118 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).. ...
119 3tzs 3tf6 Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides 2015 BE Allred, PB Rupert, SS Gauny… - Proceedings of the …, 2015 - National Acad Sciences ... molecules from available crystal structures (the structures described in this work plus PDB (41)accession ... 1 × 8U, 3FW4, 3FW5, 3HWE, 3HWF, 3HWG, 3K3L, 3PEC, 3PED, 3TF6, 3TZS, 3UOD,and ... of key calyx residues, colored as in H, isolated from the 73-structure superposition ...
120 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 ...
121 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 ...
122 3i4e 3p0x, 3oq8, 3eol, 3e5b Potential Inhibitors for Isocitrate Lyase of Mycobacterium tuberculosis and Non-M. tuberculosis: A Summary 2015 YV Lee, HA Wahab, YS Choong - BioMed Research International, 2015 - hindawi.com ... 1F8M [5]], Escherichia coli [PDB id: 1IGW [6]], Burkholderia pseudomallei [PDB id: 3I4E (paperunpublished ... crystal structure using Ligand Fit module of Discovery Studio 2.1 software (PDB id1F8M ... View at Scopus; V. Sharma, S. Sharma, KHZ Bentrup et al., “Structure of isocitrate ...
123 3kzx - Sequence specificity between interacting and non-interacting homologs identifies interface residuesa homodimer and monomer use case 2015 Q Hou, BE Dutilh, MA Huynen, J Heringa - BMC , 2015 - biomedcentral.com ... all 11 monomeric C1-type HAD Hydrolase group (2NYV, 2HSZ, 2HI0, 2AH5, 4EX6, 3MC1, 3D6J,3KBB, 3KZX, 2HDO, 3SD7). ... 6 shows the interface and predicted interface sites in the structure. ...a Secondary stucture of two chains of PDB 3QGM (chain C and D). The interface is in ...
124 3swt - Antibiotics Targeting Tuberculosis: Biosynthesis of A-102395 and Discovery of Novel Actinomycins 2015 W Cai - 2015 - uknowledge.uky.edu ... Interestingly, Cpr19 was a monomer instead of a dimer as TauD (fig 2.3.11C,PDB ID:3SWT(110)), its closest homology, suggesting that this enzyme has a distinct three dimension structure compared with other αKG:taurine dioxygenase ...
125 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 ...
126 3d64 3n58 Crystal structures of S-adenosylhomocysteine hydrolase from the thermophilic bacterium Thermotoga maritima 2015 Y Zheng, CC Chen, TP Ko, X Xiao, Y Yang… - Journal of structural …, 2015 - Elsevier ... The Refseq or PDB numbers of these sequences are: T. maritima, AAC01562.1 ... 1B3R;Trypanosoma brucei, 3H9U; M. tuberculosis, 3DHY; B. melitensis, 3N58; B. pseudomallei, 3D64.The secondary structure elements (helices (α) and strands (β)) of tmSAHH are shown above ...
127 3sbx - Proteasomal Control of Cytokinin Synthesis Protects Mycobacterium tuberculosis against Nitric Oxide 2015 MI Samanovic, S Tu, O Novák, LM Iyer, FE McAllister… - Molecular cell, 2015 - Elsevier ... The crystal structure of the Rv1205 ortholog in the close M. tuberculosis relative Mycobacteriummarinum (M. marinum) was previously crystallized (Protein Data Bank [PDB] ID: 3SBX) in aneffort by the Seattle Structural Genomics Center for Infectious Disease ...
128 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 ...
129 4iuj - Crystal structure of the RNA-dependent RNA polymerase from influenza C virus 2015 N Hengrung, K El Omari, IS Martin, FT Vreede - Nature, 2015 - nature.com ... he published fragments of FluPolA (PDB accessions 4IUJ, 4AWH, 4CB4, 3A1G and 2VY7) were fitted by eye using Coot, which was used for all model building. ...
130 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 ...
131 3nrr 3i3r Homology modeling, vasorelaxant and bradykinin-potentiating activities of a novel hypotensin found in the scorpion venom from Tityus stigmurus 2015 RJA Machado, LGM Junior, NKV Monteiro… - Toxicon, 2015 - Elsevier ... thymidylate synthase from B. bovis with dUMP, Ralitrexed and NADP (PDB ID: 3NRR, ChainA ... Protein Data Bank are listed here in increasing order of identity: X-ray structure dihydrofolatereductase/thymidylate synthase from B. bovis at 2.35 Å resolution (PDB ID: 3I3R ...
132 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 ...
133 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 ...
134 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). ...
135 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. ...
136 4gri 4g6z Dispensability of zinc and the putative zinc-binding domain in bacterial glutamyl-tRNA synthetase 2015 N Chongdar, S Dasgupta, AB Datta, G Basu - Bioscience reports, 2015 - bioscirep.org ... From extensive structural and sequence analyses from whole genome database of bacterialGluRS, we further show that in addition to many bacterial GluRS lacking a zinc-binding motif,the pZBD is actually deleted in some bacteria, all containing either glutaminyl-tRNA ...
137 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- ...
138 3ek1 3i44 Residues that influence coenzyme preference in the aldehyde dehydrogenases 2015 L González-Segura, H Riveros-Rosas… - Chemico-biological …, 2015 - Elsevier ... enzymes. 2. Methods. 2.1. Structural comparisons. Structural comparisons of the ALDHcrystal structures available in the PDB were made using PyMOL (http://www.pymol.org) and Coot [10]. 2.2. Sequence analyses. ALDH amino ...
139 3d64 3lls, 3qk8, 3ome, 3n58, 3oq8, 3myb, 3p5m, 3sll, 3i4e PEPTIDOMIMETIC COMPOUNDS 2015 RT Skerlj, AC Good - US Patent 20,150,353,606, 2015 - freepatentsonline.com ... TABLE 2. PDB ID, Key Cysteine residue. 3dp7, CYS10. 1nhw, CYS100. 1q51, CYS102. ... 1x9j,CYS227. 3n58, CYS231. 3d64, CYS238. 3ond, CYS244. ... In general the term helix or helicalis used to refer to any type of helical structure, including 3 10 -helices, -helices and -helices ...
140 4o6r 4kna, 3i44, 3ek1 Amino acid residues that affect the basicity of the catalytic glutamate of the hydrolytic aldehyde dehydrogenases 2015 RA Muñoz-Clares, L González-Segura… - Chemico-Biological Interactions, 2015 - Elsevier ... groups as sticks with carbon atoms colored depending on the structure, oxygen in ... Family organism,enzyme (PDB code), pH crystal c, pK a, Hydrogen bond d ... Burkholderia cenocepacia, BCAM0469,AMP-complex (4O6R), 6.5, 7.42, Cys302↓ Gly270↓/Lys178↓ Glu399↑ Glu476 ...
141 3k2h - Inside the biochemical pathways of thymidylate synthase perturbed by anticancer drugs: Novel strategies to overcome cancer chemoresistance 2015 L Taddia, D D'Arca, S Ferrari, C Marraccini - Drug Resistance , 2015 - Elsevier The binding sites of other folate analogs (such as methotrexate) have been studied with TS isolated from other organisms (PDB IDs: 3K2H, 1AXW) and all share the same binding site..
142 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 ...
143 3sdw - Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of Streptococcal isomerase and … 2015 Y Maruyama, S Oiki, R Takase, B Mikami… - Journal of Biological …, 2015 - ASBMB ... Owing to the high sequence identity, the overall structure of SagDhuI was highly similar to threegroup I-protein structures from S. pneumoniae (PDB code 2PPW), Novosphingobium ... In contrast,group II proteins (PDB codes 1NN4, 3K8C, 3HEE, and 3SDW), which consist of ...
144 3ief 3knu Landscape of Intertwined Associations in Multi-Domain Homo-Oligomeric Proteins 2015 SS MacKinnon, SJ Wodak - Journal of molecular biology, 2015 - Elsevier ... In addition, we identified protein structures in the PDB related to each member of our ... We examineddomain re-orientations in these relatives and how the quaternary structure is affected ... This allowedus to characterize the level of structural plasticity in protein families comprising ...
145 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 ...
146 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 ...
147 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), ...
148 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. ...
149 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 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- ...
150 3hhe 3uw1 Structural modeling and docking studies of ribose 5-phosphate isomerase from Leishmania major and Homo sapiens: A comparative analysis for Leishmaniasis … 2015 PVSZ Capriles, LPR Baptista, IA Guedes… - Journal of Molecular …, 2015 - Elsevier ... identity: 42%); (iii) 2F8M [29], the R5PI type A structure from Plasmodium falciparum (identity:35%) and (iv) 3HHE [30], the R5PI type A structure from Bartonella ... The alignment analyses showedthat no PDB sequence was able to align against the 20 C-terminal amino acids ...
151 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 ), ...
152 3k9h - Molecular anatomy of ParA-ParA and ParA-ParB interactions during plasmid partitioning 2015 A Volante, JC Alonso - Journal of Biological Chemistry, 2015 - ASBMB ... Superimposition of full-length monomer structures of δ (in green) and T thermophilus Soj (ParA-Sm) in blue (PDB: 2BEK); with P1-ParA in yellow (PDB: 3EZ6); and with TP228-ParF (ParA-Sm) in orange (PDB: 3K9H)...
153 3pgz 3lgj ENZYME CONSTRUCT 2015 A Heron, J Clarke, R Moysey… - US Patent …, 2015 - freepatentsonline.com ... In order to assess whether a suitable protein structure exists to use as a “template” to build aprotein model, a search is performed on the protein data bank (PDB) database. ... The sequencealignment and template structure are then used to produce a structural model of the ...
154 4tu1 3sth The apicomplexan glideosome and adhesins–Structures and function 2015 LE Boucher, J Bosch - Journal of structural biology, 2015 - Elsevier The apicomplexan family of pathogens, which includes Plasmodium spp. and Toxoplasma gondii,are primarily obligate intracellular parasites and invade multiple c.
155 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 ...
156 3pgz 3lgj MODIFIED HELICASES 2015 A Heron, J Clarke, R Moysey… - US Patent …, 2015 - freepatentsonline.com ... In order to assess whether a suitable protein structure exists to use as a “template” to build aprotein model, a search is performed on the protein data bank (PDB) database. ... The sequencealignment and template structure are then used to produce a structural model of the ...
157 4qfh - Ligand docking and binding site analysis with pymol and autodock/vina 2015 MA Rauf, S Zubair, A Azhar - International Journal of Basic and …, 2015 - sciencepubco.com ... In recent years, the process of virtual screening technique for docking small molecules into aknown protein structure is a powerful tool for drug ... Enter the name of Protein or enzyme that willbe used for docking studies (For example, Glucose 6 Phosphate or its pdb id 4QFH). ...
158 2mj3 - Structural and functional characterisation of ferredoxins in Bacillus cereus 2015 S Monka - 2015 - duo.uio.no ...as well as testing out models generated from several homologous PDB-structures. This server generated models from 10 PDB files (1I7H, 3AH7, 3ZYY, 1KRH, 3N9Z, 2MJ3, 3HUI, 2Y5C, 1JQ4, 2WLB15) and generated two models from each by using two different programs SCULPTURE and MOLREP. ...
159 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 ...
160 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 ...
161 3p4i 4dq8 Mycobacterium tuberculosis kinases as potential drug targets: production of recombinant kinases in E. coli for functional characterization and enzyme inhibition 2015 V Lukman - 2015 - uir.unisa.ac.za ... Other mycobacterial AKs have been deposited in the Protein Data Bank (www.pdb.org), with high levels of similarity to the putative Mtb AK (M. avum, pdb 3P4I at 74.4% and M. marinum pdb 4DQ8 at 75.1%). ...
162 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 ...
163 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 ...
164 4efz - Characterizations of Two Bacterial Persulfide Dioxygenases of the Metallo-β-lactamase Superfamily 2015 SA Sattler, X Wang, KM Lewis, PJ DeHan… - Journal of Biological …, 2015 - ASBMB ... The statistics for the diffraction data are listed in Table 1. Initial phasing of apo- form PpPDO2diffraction data was conducted by molecular replacement with the PDB coordinates of model4EFZ using PHENIX Phaser (18). ... RESULTS Global Structure ...
165 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 ...
166 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..... ...
167 4qhq - The contribution of methionine to the stability of the Escherichia coli MetNIQ ABC transporter-substrate binding protein complex. 2015 PT Nguyen, QW Li, NS Kadaba, JY Lai, JG Yang… - Biological …, 2015 - degruyter.com ... structures with PDB entries 3TQW, 3UP9, 4EF1, 4GOT, 4IB2, 4K3F, 4QHQ, 4QYM, and 4Q5T. ...2008) that was in turn solved by molecular replacement from PDB entry 1P99 (Williams et al.,2004), a Gly-Met-binding protein. ... Coordinates and structure factors have been ...
168 3eg4 3mdx, 3qxi, 3lqw, 3laa, 3oc7 Nouvelles méthodes de calcul pour la prédiction des interactions protéine-protéine au niveau structural 2015 P Popov - 2015 - theses.fr ... au niveau structural Thèse soutenue publiquement le « 28 Janvier 2015 », devant le jury composéde : ... blue, respectively). Right: native structure of Target 58 (grey) and medium-quality model pro- ...18 2.2 Query protocols for the PDB that were used to compose the bound bench- ...
169 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 ...
170 3m1x - Protein structure prediction guided by crosslinking restraints–A systematic evaluation of the impact of the crosslinking spacer length 2015 T Hofmann, AW Fischer, J Meiler, S Kalkhof - Methods, 2015 - Elsevier ... Based on the structure of calmodulin (PDB entry 2ksz) the average Cβ–Nz, Cβ–Cγ, Cβ–Cδ,Cβ–N H2 , and Cβ–S G distances ... Structure, Uniprot, Resolution [Å], Molecular weight [Da],Sequence length [aa], Lys portion [%], α-helix [%], β-sheet ... 3m1x, C4LXT9, 1.2, 15882, 138, 7, ...
171 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). ...
172 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 ...
173 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. ...
174 3hgb - Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens 2015 JGM Rack, R Morra, E Barkauskaite, R Kraehenbuehl… - Molecular cell, 2015 - Elsevier ... SpyGcvH-L structure is shown in black and canonical GcvH of cattle (PDB: 3KLR), pea (PDB: 1DMX), and M. tuberculosis (PDB: 3HGB) in orange, green, and yellow, respectively. Residue numbers for GcvH-L are given. ...
175 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 ...
176 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. ...
177 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 ...
178 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 ...
179 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 ...
180 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% ...
181 4h51 - Structural basis for the relaxed substrate selectivity of Leishmania mexicana broad specificity aminotransferase 2015 J Wen, C Nowicki, W Blankenfeldt - Molecular and biochemical , 2015 - Elsevier ... The most similar structure, however, is that of a putative aspartate aminotransferasefrom Leishmania major Friedlin (LmajASAT, PDB entry 4H51 [16]), which was notavailable when we first determined the structure of LmexBSAT. ...
182 4pca - Structure and Biophysical Characterization of the S-adenosylmethionine Dependent O-methyltransferase PaMTH1, a Putative Enzyme Accumulating during … 2015 D Chatterjee, D Kudlinzki, V Linhard, K Saxena… - Journal of Biological …, 2015 - ASBMB ... α2 Page 7. Structure and Biophysical characterization of PaMTH1 7 loop ... Arg232, Asp235).CCoAOMT (Medicago sativa) is (PDB:1SUI) one of the closest structural homologueof PaMTH1 and also crystallizes as a dimer. The dimerization ...
183 4qhq - The I-TASSER Suite: protein structure and function prediction 2015 J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang - Nature methods, 2015 - nature.com ... binding protein from Burkholderia cenocepacia bound to methionine (CAMEO: C0081; PDB:4qhqA) (e ... bound to calcium ion and thymidine-3′,5′-diphosphate (CAMEO: C0046; PDB:4qf4A ... on the significance of threading alignments and the density of structure clustering; the ...
184 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 ...
185 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 ...
186 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 .... ...
187 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. ...
188 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. ...
189 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 ...
190 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 ...
191 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 ...
192 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: ...
193 4wkw - The redox state regulates the conformation of Rv2466c to activate the antitubercular prodrug TP053 2015 D Albesa-Jov, N Comino, M Tersa, E Mohorko - Journal of Biological , 2015 - ASBMB ...E, schematic representation showing the comparison between the crystal structure of Rv2466c-CT-His and the structural homologue from M. leprae (PDB code 4WKW). The canonical thioredoxin folds are shown in orange. The α-helical subdomains of Rv2466c-CT-His and the M. leprae homologue ...
194 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 ...
195 3men - Homology modeling of parasite histone deacetylases to guide the structure-based design of selective inhibitors 2015 J Melesina, D Robaa, RJ Pierce, C Romier - Journal of Molecular , 2015 - Elsevier ... Wizard (Schrdinger Inc.) by adding hydrogen atoms, defining the protonation states of residuesand minimising the structure to remove steric ... Number, Organism/protein name, Abbreviation,PDB ID. ... 10, Burkholderia pseudomallei acetylpolyamine aminohydrolase, BpAPAH, 3MEN ...
196 4o3v 4lso, 4mei, 4jf8, 4kz1, 4nhf Molecular and structural analysis of Legionella DotI gives insights into an inner membrane complex essential for type IV secretion 2015 T Kuroda, T Kubori, XT Bui, A Hyakutake, Y Uchida… - Scientific reports, 2015 - nature.com ... (PDB ids 4JF8, 4KZ1, 4LSO, 4MEI, and 4NHF) and Richettsia typhi (4O3V) were published in PDB database. The arrangement of the VirB8 secondary structure isessentially the same as that of DotI C except for α3 and α5 (Fig. ...
197 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 ...
198 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. . ...
199 3gtd 3tv2, 3rd8, 3rrp, 3qbp, 3ome, 3oc7, 3njb, 3njd, 3myb, 3moy, 3he2, 3h81, 4qfe Stereochemistry of enzymatic water addition to C= C bonds 2015 BS Chen, LG Otten, U Hanefeld - Biotechnology Advances, 2015 - Elsevier ... Entry, Name (EC-number), Sources (PDB-number), Types of reaction, Cofactor, Regio- andstereoselectivity. ... sapiens (3E04) Mycobacterium abscessus (3RRP) Sinorhizobium meliloti (4HGV)Thermus thermophilus (1VDK) Rickettsia prowazekii (3GTD) Mycobacterium tuberculosis ...
200 3rd5 - Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells 2015 M Abu-Remaileh, E Joy-Dodson - Journal of Biological , 2015 - ASBMB ... B, a structural model of the SDR region (generated by the RosettaCM protocol as implemented by the Robetta server (78), starting from PDB ID 3rd5 (58) as a template structure) shows an extended central β sheet formed by Rossmann folds. ...
201 4iv5 - From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases 2015 D Shi, NM Allewell, M Tuchman - International Journal of Molecular …, 2015 - mdpi.com ... dodecameric holoenzyme with DHOase, were determined [50,51]. Only one eukaryotic ATCasestructure, of Trypanosoma cruzi, has been determined (PDB code: 4IV5). ... Both domains havean αβα structure with a parallel β-sheet in the center and α helices on both sides. ...
202 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 ...
203 3q8n - Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications 2015 F Steffen-Munsberg, C Vickers, H Kohls, H Land… - Biotechnology …, 2015 - Elsevier In this review we analyse structure/sequence-function relationships for the superfamily ofPLP-dependent enzymes with special emphasis on class III transaminase.
204 3u0i - SequenceStructureFunction Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria 2015 FH Ahmed, PD Carr, BM Lee, L Afriat-Jurnou - Journal of molecular , 2015 - Elsevier ... SequenceStructureFunction Classification of a Catalytically Diverse OxidoreductaseSuperfamily in ... Functional annotation using phylogenetic, structural, and spectroscopic methodsrevealed their ... Four novel crystal structures show that plasticity in substrate binding pockets ...
205 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 ...
206 4qic - General Stress Signaling in the Alphaproteobacteria 2015 A Fiebig, J Herrou, J Willett - Annual review of genetics, 2015 - annualreviews.org ... (f) Structural representation of full-length PhyR in an open conformation bound to NepR(PDB:4QIC). This complex structure evinces an unusual exchange of receiver domain secondaryelements 5-12 (yellow) between adjacent PhyR/NepR complexes in the crystal lattice. ...
207 4pq9 - Crystal structural basis for Rv0315, an immunostimulatory antigen and inactive beta-1, 3-glucanase of Mycobacterium tuberculosis 2015 W Dong, J Huang, Y Li, Y Tan, Z Shen, Y Song - Scientific , 2015 - ncbi.nlm.nih.gov ... was solved at a resolution of 1.7 by molecular replacement using the structure of-1,3-glucanase from Mycobacterium marinum (PDB code 4PQ9) as a ... Other than the differentsize of the cavity, the overall structure of Rv0315 was similar to that of ZgLamA GH16 (Fig. ...
208 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 ...
209 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)...
210 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, ...
211 4kyx - Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2 2015 M Carter, AS Jemth, A Hagenkort, BDG Page… - Nature …, 2015 - nature.com ... The structure was solved by molecular replacement of the template structure file with PDB ID 4KYX using MolRep, and Arp/wARP was used for building the initial model, followed by iterative building cycles using the Refine program in Phenix ...
212 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. ...
213 4k9d - Surface-displayed glyceraldehyde 3-phosphate dehydrogenase and galectin from Dirofilaria immitis enhance the activation of the fibrinolytic system of the host 2015 J González-Miguel, R Morchón, M Siles-Lucas… - Acta tropica, 2015 - Elsevier ... msa/clustalw2/) and prediction of the secondary structures and three-dimensional modeling with the Swiss-Model server ( Arnold et al., 2006; http://swissmodel.expasy.org/) using as templates the X-ray crystal structure of a GAPDH from B. malayi (code pdb: 4K9D) for DiGAPDH ...
214 3gp5 4dz6, 3gw8 Vanadium and proteins: Uptake, transport, structure, activity and function 2015 JC Pessoa, E Garribba, MFA Santos… - Coordination Chemistry …, 2015 - Elsevier ...A more recent 2.2 Å structure of a transition state nucleoside diphosphate kinase from Borrelia burgdorferi bound to vanadate(V) and ADP was deposited (PDB: 4DZ6) ... Later the structure of the bacterial dPGM from Burkholderia pseudomallia was also solved complexed with vanadate(V) (PDB: 3GW8 and 3GP5) [319]; in the 3GW8 structure at 1.9 Å resolution, glycerol, from the crystallization conditions, reacted with vanadate(V) forming a species quite similar to the enzymatic substrate. ...
215 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 ...
216 2lwk - Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions 2015 YZ Shi, L Jin, FH Wang, XL Zhu, ZJ Tan - Biophysical journal, 2015 - Elsevier TABLE 1 The 32 RNA Molecules for 3D Structure Prediction in This Work 26 2LWK ...
217 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 ...
218 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 ...
219 3d5t - Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures 2015 S Shokrollahzade, F Sharifi, A Vaseghi… - Journal of theoretical …, 2015 - Elsevier ... Mesophilic, Burkholderia pseudomallei, 3D5T/A, 2.51. ... Fig. 1. The structure ofadenylate kinases from the psychrophile Bacillus globisporus (PDB ID: 1S3G). ... Thestructure is shown as surface representation by Pymol software. ...
220 3k2h - Characterization of natural product biological imprints for computer-aided drug design applications 2015 N Sturm - 2015 - theses.fr ... Changes in sequence and structure also explain the poor similarity between SB4 inhibitor-binding sites in Mitogen-activated protein (MAP) kinase 14 and MAP kinase 1 (PDB codes: 1bl7, 3erk), and between the antifolate LYA-binding site in human and protozoan thymidylate synthases (PDB codes: 1juj, 3k2h). ...
221 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. ...
222 3eiz - Influence of azide incorporation on binding affinity by small papain inhibitors 2014 AEM Wammes, TG Hendriks - Bioorganic & medicinal , 2014 - Elsevier ... 20 (b) Docking of leupeptin in the active site of papain (PDB file 1POP). ... 21 Prior to docking we investigated different papain structures of the PDB to explore different ligandpapain complexes, as well as the flexibility of the protein in the area of the binding site. ...
223 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 ...
224 4fzi - < i> Trypanosoma cruzi</i> chemical proteomics using immobilized benznidazole 2014 A Trochine, G Alvarez, S Corre, P Faral-Tello - Experimental , 2014 - Elsevier ... Murta et al., 2006). In addition, TcOYE and TcAKR have equivalent tertiary structures. TcAKR was crystallized in the apo form and its structure was recently deposited at a 2.6 resolution [PDB: 4fzi]. The protein has an (alpha ...
225 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),...
226 3ek2 - Paclitaxel Induces Apoptosis in Breast Cancer Cells through Different Calcium-Regulating Mechanisms Depending on External Calcium Conditions 2014 Z Pan, A Avila, L Gollahon - International journal of molecular sciences, 2014 - mdpi.com ... 3 2i6x ?10.3 Porphyromonas gingivalis hydrolase 4 3ek2 ?10.3 Burkholderia pseudomallei eonyl reductase ... Two libraries, ?pdb_subset.py? and ?pdb_centermass.py? from the pdb-tools project (https://code.google.com/p/pdb-tools/) were modified and used in Artemis. ...
227 4lsm - Biochemical characterisation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the liver fluke, Fasciola hepatica 2014 VL Zinsser, EM Hoey, A Trudgett, DJ Timson - Biochimica et Biophysica …, 2014 - Elsevier ... other parasites, for example Plasmodium falciparum (PDB: 1YWG [52]; rmsd 1.226 Å over 8358equivalent atoms) Trypanosoma brucei (PDB: 2X0N, [53]; rmsd 2.009 Å over 8522 equivalentatoms) and Trypanosoma cruzi (PDB: 4LSM, note that this structure only contains ...
228 4ix8 - Tyrosine aminotransferase from< i> Leishmania infantum</i>: A new drug target candidate 2014 MA Moreno, A Alonso, PJ Alcolea, A Abramov - International Journal for , 2014 - Elsevier ... code: 3DYD) and the mouse TAT (PDB code: 3PDX) ( Mehere et al., 2010). Recently, the structure of LiTAT has been solved to 2.3 (PDB code: 4IX8) ( Moreno et al., 2014). On the basis of this background, the aim of the work is ...
229 3gwc - PREDICTION OF BINDING ENERGIES/INTERACTIONS BETWEEN DIOSPYRIN AND DIFFERENT TARGET PROTEINS OF Mycobacterium tuberculosis BY IN SILICO MOLECULAR DOCKING STUDIES 2014 AJ Suresh, R Devi, KM Noorulla - Indo American Journal of Pharmaceutical Research, 2014 - ejmanager.com ... Protein Data Bank (PDB) ID were selected, NADH-dependent enoyl- ACP reductase (InhA) - 2NSD, Adenosine kinase (Adok) - 2PKK, Mycolic acid synthase (PcaA) - 1L1E, Lysine N- acetyltransferase (MbtK) - 1YK3, Thymidylate synthase X (ThyX) - 3GWC, Thymidylate kinase ...
230 3laa - A domain dictionary of trimeric autotransporter adhesins 2014 J Bassler, BH Alvarez, MD Hartmann… - International Journal of …, 2014 - Elsevier ... Name, Description, Topological crossover, PDB. Anchor, Trimeric, 12-stranded outermembrane β-barrel, –, 2gr7. Stalk, Slender segment of predominantly coiled-coil structure, –, ...Long neck, Neck variant of 22 residues length, 120° cw, 3laa. ...
231 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 ...
232 3f0g - Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment 2014 J Kalinowska-T, PK Fyfe, A Dawson and WN Hunter - BMC Structural Biology, 2014 - biomedcentral.com ... Structural comparisons of IspF orthologues from the Protein Data Bank (PDB) were carried out using the DALI server [28]. Pairwise sequence identities range from 28 to 90%, Z scores from 18 to 31 and RMSD values from 0.3 to 2.5 ?. ...
233 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
234 3kx6 - Structural and Functional Divergence of the Aldolase Fold in Toxoplasma gondii 2014 ML Tonkin, AS Halavaty, R Ramaswamy, J Ruan… - Journal of molecular …, 2014 - Elsevier ... We also determined the structure of TgDPA in a different crystal form (data not shown but structuredeposited with identifier PDB ID 3QYQ ... However, preliminary sequence and structural comparisonof several dR5P aldolases (rmsd of < 2.0 Å and sequence homology as low ...
235 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 ...
236 3jst - Interactions with the Bifunctional Interface of the Transcriptional Coactivator DCoH1 Are Kinetically Regulated 2014 D Wang, MW Coco, RB Rose - Journal of Biological Chemistry, 2014 - ASBMB ... The prokaryotic and archaeal PCD are obligate dimers ((19) and pdbid 3jst, 2ebb, 1uso ... with theCCP4 program Phaser (30) using the 1.6 Å wild-type DCoH2 structure (PDB ID: 1RU0 ... asymmetricunit, forming a tetramer with a symmetry-related dimer (1). The structure is identical ...
237 4g6z 4gri Evolutionary insights about bacterial GlxRS from whole genome analyses: is GluRS2 a chimera? 2014 S Dasgupta, G Basu - BMC evolutionary biology, 2014 - biomedcentral.com ... The structure shown on the left corresponds to the crystal structure of T. thermophilus GluRS (pdb ID: 1j09) with residues 1-322 and 323-468 comprising the N- and the C-terminal domains, respectively. Is GluRS2 a chimera? ...
238 3eiy - Asn112 in< i> Plasmodium falciparum</i> glutathione S-transferase is essential for induced reversible tetramerization by phosphate or pyrophosphate 2014 I Quesada-Soriano, C Barn, R Tllez-Sanz - et Biophysica Acta (BBA , 2014 - Elsevier ... the alignment between one of the docking poses for the binding of pyrophosphate to the PfGST tetramer near the Asn112–Lys117 closed-square pattern and three of the pyrophosphatase structures (3Q4W from Thermococcus thioreducens, 3EIY from Burkholderia pseudomallei and 2AUU/1I6T from E. coli), is suspiciously good. ...
239 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 ...
240 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 ...
241 3laa - Haemophilus influenzae surface fibril (Hsf) is a unique twisted hairpin-like trimeric autotransporter 2014 B Singh, T Al Jubair, M Mörgelin, A Sundin… - International Journal of …, 2014 - Elsevier ... The templates are presented as Hsf amino acids (PDB code of template: identity/similarity, gap),0136 ... 1863–2023 (1s7m: 73/79, 3), 2024–2143 (2qih: 11/23, 0), 2144–2315 (3laa: 15/22 ... A domain close to the C-terminal (2144–2315 aa) was constructed from PDB:3laa with low identity, but having a high local similarity. ...
242 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
243 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. ...
244 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 ...
245 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 ...
246 3ezn - Mechanism of Dephosphorylation of Glucosyl-3-phosphoglycerate by a Histidine Phosphatase 2014 Q Zheng, D Jiang, W Zhang, Q Zhang, Q Zhao - Journal of Biological Chemistry, 2014 - ASBMB ... 2B). Other significant structural matches included phosphoserine phosphatase 1 (34) (PsP1; Protein Data Bank code 4IJ5) and phosphoglycerate mutase (35) (PGM; Protein Data Bank code 3EZN). ... PDB, Protein Data Bank. ...
247 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). ...
248 3p96 - High Throughput Screen Identifies Small Molecule Inhibitors Specific for Mycobacterium tuberculosis Phosphoserine Phosphatase 2014 G Arora, P Tiwari, RS Mandal, A Gupta - Journal of Biological Chemistry, 2014 - ASBMB ... not available. The closest homolog for SerB2 protein was SerB protein from Mycobacterium avium (Protein Data Bank code 3P96) with 84% sequence identity, 99% query coverage, and an E value of 0.0. The superimpositions ...
249 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. ...
250 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. ...
251 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 ...
252 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) ...
253 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%). ...
254 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). ...
255 3py6 - Computational analysis of N-H...PI interactions and its impact on the structural stability of beta-lactamases 2014 P Lavanya, S Ramaiah, A Anbarasu - Computers in Biology and Medicine, 2014 - Elsevier ... Three dimensional structures of ?-lactamases were retrieved from Protein Data Bank (PDB) [26]. ... The PDB codes of selected 67 ?-lactamases in the dataset are as follows: ... A, 3IF6-A, 3L6N-A, 3LVZ-A, 3LY3-A, 3M2K-A, 3OPL-A, 3OZH-A, 3P09-A, 3PAE-A, 3PG4-A, 3PY6-A, 3QI0-A ...
256 3enk - Functional characterization and transcriptional analysis of galE gene encoding a UDP-galactose 4-epimerase in Xanthomonas campestris pv. campestris 2014 CT Li, CT Liao, SC Du, YP Hsiao, HH Lo… - Microbiological …, 2014 - Elsevier ... based on the detection of hydrogen bonds defined by an electrostatic criterion using the Dictionaryof Protein Secondary Structure database method obtained from PDBsum database. Thethree-dimensional structural model of Xcc GalE was based on E. coli GalE (PDB ID 1XEL ...B. pseudomallei (Bps-GalE, PDB code 3ENK); B. anthracis (Ban-GalE, PDB code 2C20); and T. thermophilus (Tth-GalE, PDB code 2P5U)...
257 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 ...
258 3gmt - Adenylate kinase from< i> Streptococcus pneumoniae</i> is essential for growth through its catalytic activity 2014 TT Thach, TT Luong, S Lee, DK Rhee - FEBS Open Bio, 2014 - Elsevier ... Open, ligand-free SpAdK structure was solved by molecular replacement using PHENIX [35] with AdK from Marinibacillus marinus (PDB ID: 3FB4) and Burkholderia pseudomallei (PDB ID: 3GMT) as search models. ...
259 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 ...
260 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 ...
261 3mc4 - Crystal structure of serine acetyl transferase from< i> Brucella abortus</i> and its complex with coenzyme A 2014 S Kumar, N Kumar, N Alam, S Gourinath - Biochimica et Biophysica Acta ( , 2014 - Elsevier ... max SAT [10] have been previously published. The coordinates of a crystal structure of SAT from Brucella melitensis has also been deposited at the Protein Data Bank (PDB code: 3MC4). SATs from E. coli, B. melitensis, H. influenzae ...
262 3nwo - The crystal structure of the amidohydrolase VinJ shows a unique hydrophobic tunnel for its interaction with polyketide substrates 2014 Y Shinohara, A Miyanaga, F Kudo, T Eguchi - FEBS letters, 2014 - Elsevier ... method using the Molrep program [16], with the crystal structure of the putative proline iminopeptidase Mycobacterium smegmatis (PDB code: 3NWO) being used ... The resulting coordinates and structure factors have been deposited in the Protein Data Bank (PDB code: 3WMR) ...
263 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.
264 3jst - Structure and identification of a pterin dehydratase-like protein as a RuBisCO assembly factor in the alpha-carboxysome 2014 NM Wheatley, CD Sundberg, SD Gidaniyan? - Journal of Biological Chemistry 2014 - ASBMB ... diagram. Coordinates and structure factors have been deposited with the PDB ID code 4LOW. ... carboxysome). Data deposition - Atomic coordinates and diffraction data for acRAF have been deposited in the PDB with ID 4LOW. ...
265 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. ...
266 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 ...
267 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. ...
268 3v2i - Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Å resolution shows the closed structure of the substrate-binding cleft 2014 A Singh, L Gautam, M Sinha, A Bhushan, P Kaur… - FEBS open bio, 2014 - Elsevier ... 27], Francisella tularensis (FtPth) (PDB: 3NEA) [28] and Burkholderia thailandensis (BtPth) (PDB:3V2I) [29]. ... tripeptide (grey) from the neighbouring molecule from the structure of EcPth (PDB ID:2PTH ... with the stereochemistry of the substrate binding cleft in the structure of SpPth ...
269 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 ...
270 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. ...
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 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) ...
273 3ek2 - Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (ACP) Reductase Inhibitor 2014 J Schiebel, A Chang, S Shah, Y Lu, L Liu, P Pan - Journal of Biological Chemistry, 2014 - ASBMB ... Molecular replacement was performed in Phaser using the PDB entry 3EK2 as a template. ... The structure factors and coordinates of the different FabI structures have been deposited in the ProteinData Bank with the PDB entry codes 4CUZ (saFabI-NADPH-PT173), 4CV1 ...
274 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. ...
275 3rd5 - Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family 2014 NTN Tang, L Le - Evolutionary bioinformatics online, 2014 - ncbi.nlm.nih.gov ... structures within each group were compared with each other and the selected structure was the ...GROUPS, PDB CODE AND NAME OF REPRESENTATIVE STRUCTURES. ... 4, 3rd5 chain A, aputative uncharacterized oxidoreductase protein from Mycobacterium Paratuberculosis. ...
276 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 ...
277 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+ ...
278 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 ...
279 3rr2 - Structural and biochemical analyses of< i> Microcystis aeruginosa</i> O-acetylserine sulfhydrylases reveal a negative feedback regulation of cysteine biosynthesis 2014 M Lu, BY Xu, K Zhou, W Cheng, YL Jiang? - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014 - Elsevier ... The sequences are (PDB codes in parentheses) Mycobacterium tuberculosis OASS (2Q3D), Haemophilus influenzae OASS (1Y7L), Salmonella typhimurium OASS (1OAS), Mycobacterium marinum Atcc Baa-535 OASS (3RR2), Thermotoga maritima OASS (3FCA), Arabidopsis ...
280 3gmt - Sampling large conformational transitions: adenylate kinase as a testing ground 2014 SL Seyler, O Beckstein - Molecular Simulation, 2014 - Taylor & Francis Out of these structures only four (PDB IDs 4ake, 2rh5, 3umf, 3gmt) were crystallised in the apo form, i.e. in the absence of a substrate-like ligand, and these structures represent the open conformations of AdK.
281 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 ...
282 4i1v 4i1u Crystal structure of Legionella pneumophila dephospho-CoA kinase reveals a non-canonical conformation of P-loop 2014 X Gong, X Chen, D Yu, N Zhang, Z Zhu, L Niu… - Journal of structural …, 2014 - Elsevier ... The first DPCK crystal structure was solved and reported from Haemophilus influenzae (HiDPCK,PDB code 1jjv ( Obmolova et al ... DPCK structures are also available in the PDB, such asBurkholderia vietnamiensis DPCK (BvDPCK, PDB codes 4i1u, 4i1v, Seattle Structural ...
283 3khw - 3D protein structure prediction of influenza A virus based on optimization genetic algorithm. 2014 J Gao, PX Jin, HX Xu - Pakistan journal of pharmaceutical sciences, 2014 - pjps.pk ... acid residues Sixty groups of influenza A (H1N1) virus protein were selected from PDB database, 3HTO, 4F15, 3B7E, 3BEQ, 3HTP, 3HTQ, 3HTT, 4EDB, 4B7N, 4B7M, 3M5R, 3M8A, 3LKN, 3QQ4, 3QQ3, 3TI3, 3LZF, 3M6S, 3UBE, 3UBJ, 3UBN-A, 4D9J, 3GBN, 3KHW, 4EDA, 2ZKO ...
284 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. ...
285 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);...
286 3gka - Estudo estrutural das enzimas Topoisomerase II Mitocondrial e Old Yellow Enzyme de Trypanosoma cruzi 2014 NC Rodrigues - teses.usp.br ... resolution of 1.27 and 2.00 , respectively. The atomic coordinates and structure factors of the TcOYE structure in P212121 and P21 crystalline forms have been deposited in the Protein DataBank with the accession codes 4E2B and 4E2D, respectively. TcOYE displays a ...
287 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 ...
288 3ido 3jvi Atomic resolution crystal structure of< i> Vc</i> LMWPTP-1 from< i> Vibrio cholerae</i> O395: insights into a novel mode of dimerization in the Low molecular Weight 2014 S Nath, R Banerjee, U Sen - Biochemical and Biophysical Research , 2014 - Elsevier ... Several structures of LMWPTP from eukaryotic organism such as human- HCPTPA (PDB: 5PNT) [4], bovine BPTPA (PDB: 1Z12) [5], mouse RPTPA (PDB: 2P4U) [6], yeast LTP1 (PDB: 1D1P) [7] and protozoan parasite Entameoba histolytica EhPtp (PDB: 3IDO) [8] are ...
289 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 ...
290 4pq9 - A sweet new wave: structures and mechanisms of enzymes that digest polysaccharides from marine algae 2014 JH Hehemann, AB Boraston, M Czjzek - Current opinion in structural , 2014 - Elsevier ... CAZy family, Protein, PDB codes. GH16, -Carrageenase (Pseudoaltermonas carragenovora), 1DYP. -Agarase ... -Porphyranase B (Zobellia galactanivorans), 3JUU. -1,3-Glucanase (Mycobacterium marinum M), 4PQ9. Laminarinase (Thermotoga ...
291 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 ...
292 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]. ...
293 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 ...
294 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 ...
295 3uam - Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases 2014 AJ Book, RM Yennamalli, TE Takasuka - Biotechnology for , 2014 - ncbi.nlm.nih.gov ... These are from Hypocrea jecorina (Trichoderma reesei, Protein Data Bank (pdb) id: 2VTC) [24], Thielavia terrestris (pdb id: 3EII) [7 ... pdb id: 2BEM) [25], Vibrio cholerae O1 biovar EI Tor (pdb id: 2XWX) [26], Burkholderia pseudomallei (pdb id: 3UAM), and Enterococcus faecalis ...
296 4k73 - Stratégies d'optimisation des bêta-lactamines pour le traitement des infections dues aux mycobactéries multirésistantes 2014 V Dubée - 2014 - theses.fr ... 20 Tableau 3. Structures de L,D-transpeptidases inscrites dans la Protein Data Bank. ... Figure 1.Structure des classes les plus fréquemment utilisées de β-lactamines. ... accepteur. La pénicillineest un analogue structural de cette extrémité D-Ala–D-Ala, et pourrait donc former un ...
297 3ecd 3h7f A novel serine hydroxymethyltransferase from Arthrobacter nicotianae: characterization and improving catalytic efficiency by rational design 2014 W Jiang, L Chen, S Yuan, B Li, Z Liu - BMC biotechnology, 2014 - biomedcentral.com ... directed mutagenesis was indicated on the three-dimensional structure of AnSHMT, which wasconstructed from the known x-ray structure of Burkholderia Pseudomallei MycobacteriumTuberculosis T.Th.Hb8 (PDB entry 3H7F, 2DKJ and 3ECD) using Swiss ...
298 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 ...
299 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 ...
300 3gp5 - Vanadate in structural biology 2014 S Akabayov, B Akabayov - Inorganica Chimica Acta, 2014 - Elsevier ... Protein data bank; Data mining; Protein-vanadate complex. ... Structures of biological macromolecules containing ligands with vanadium were downloaded from the Protein Databank (www.pdb.org ... PDB, ProteinOrganism, CLASS a, Geometry b, DNA/RNA c, Metal Ion d, TS e, Ligand ...
301 3nxs - Strategies for purifying variants of human rhinovirus 14 2C protein 2014 T S?ra, R Konrat, T Skern - Protein expression and purification, 2014 - Elsevier ... Score, Entry name, PDB identifier. 6198, Human nuclear valosin containing protein like (Nvl), C-terminal AAA?ATPase domain, 2X84. ... 2887, Crystal structure of LAO/AO transport system from Mycobacterium smegmatis bound to GDP, 3NXS. ...
302 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 ...
303 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 ...
304 4fkx - Insights into mechanism kinematics for protein motion simulation 2014 M Diez, V Petuya, LA Martnez-Cruz - BMC , 2014 - biomedcentral.com ... obtained results have been compared with each proteins' structural data, available on the ProteinData Bank (PDB). The results are shown on Table 2. ... mass (Da) in secondary structures secondary structures (PDB) -helix -sheet -helix -sheet ... 4fkx 55.13 34.8 19.7 42 16 ...
305 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 ...
306 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 ...
307 3lg6 - Molecular dynamics for computational proteomics of methylated histone H3 2014 C Grauffel, RH Stote, A Dejaegere - Biochimica et Biophysica Acta (BBA)- …, 2014 - Elsevier ... This analysis is made possible by the substantial amount of structural information available oncomplexes between PHD domains and modified histone tails. ... Protein Data Bank IDs are indicated,and NMR structures are labeled with a (*). Protein name, Ref. ... PDB structure. ...
308 3p96 3km3, 3k9g Macromolecular X-ray structure determination using weak, single-wavelength anomalous data 2014 G Bunkóczi, AJ McCoy, N Echols… - Nature …, 2014 - nature.com ... phasing, accounting for 73% of such structures deposited in the Protein Data Bank (PDB;http://www.pdb.org/) 1 in 2013. In the SAD method, the X-ray diffraction from anomalouslyscattering atoms in a molecule provides X-ray phase information for the entire crystal structure ...
309 3gaf - Carboxyl-Terminal and Arg38 are Essential for Activity of the 7α-Hydroxysteroid Dehydrogenase from Clostridium absonum 2014 D Lou, B Wang, J Tan, L Zhu - Protein and peptide letters, 2014 - ingentaconnect.com ... E. coli (Ec 7α-HSDH, PDB code: 1FMC) [21] and Brucella melitensis (PDB code: 3GAF) havebeen ... and arginine at position 37 of the human estro- genic 17β-HSDH (PDB code: 1QYV ... 38 isof vital importance, and the residue- replacement disrupts the normal structure for cofactor ...
310 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 ...
311 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 ...
312 3eiz 3i4t High pKa variability of cysteine residues in structural databases and the effect of H-bond contributions 2014 SM Marino, İ Soylu - Türk Biyokimya Dergisi [Turkish Journal of …, 2014 - turkjbiochem.com ... High pKa variability of cysteine residues in structural ... RESULTS of ppka3 on PDB-crystal datasetprot=protein name res_num=residue number H-bond=hydrogen bond contribution to pKaprediction (pKa) Coul=electrostatics (from Coulombic interactions) contribution to pKa ...
313 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, ...
314 3f9i - Education Corner 2014 J Beckham - Newsletter, 2014 - rcsb.org ... that organism that is essential for survival or virulence (eg fatty acid biosynthesis enzymes 3F9I, dihydrofolate reductases 3DAT, or host-pathogen signaling phosphatases 2Y2F). The students narrow their selection by those enzyme which have an available PDB crystal structure ...
315 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 ...
316 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 ...
317 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 ...
318 2kz0 2mcq Structural and spectroscopic insights into BolA-glutaredoxin complexes 2014 T Roret, P Tsan, J Couturier, B Zhang - Journal of Biological Chemistry, 2014 - ASBMB ... and the AtGrxS14-BolA2 apo-heterodimer model (2MMA) are available at the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank. ... Accordingly, in Ehrlichia chaffeensis and Rickettsia prowazekii BolA structures (PDB entry 2KZ0 and 2MCQ ...
319 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 ...
320 3gtd 3rrp, 3qbp Structural and functional characterization of Trypanosoma cruzi fumarate hydratase isoforms 2014 RAP de Pdua - teses.usp.br ... TcFHs structural models, built by homology modeling using the Leishmania major fumarase crystalstructure as template, were compared to ... Keywords: fumarase, fumarate hydratase, Chagas disease,selective inhibitors, crystal structure. ... The fainter structures correspond to the ...
321 4hec - Structure and Function of RNase AS, a Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence In Vivo 2014 M Romano, R van de Weerd, FCC Brouwer - Structure, 2014 - Elsevier ... Structural features of the enzyme resemble those of an independently determined structure reported in the Protein Data Bank while our functional characterization was ongoing (PDB code 4HEC) (Abendroth et al., 2014). ...
322 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. ...
323 3uf8 - Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus 2014 C Leyrat, M Renner, K Harlos, JT Huiskonen? - Structure, 2013 - Elsevier ... HMPV M was solved at 2.8 ? resolution by molecular replacement using the structure of RSV M (Protein Data Bank ID [PDB ID] 2VQP; sequence identity, 38%). Data collection and refinement statistics are given in Table 1 (R work = 0.19; R free = 0.23). Table 1. ...
324 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. ...
325 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 ...
326 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). ...
327 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 ...
328 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...
329 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. ...
330 3ixc 3oi9, 3mxu, 3laa, 3mdx, 3m1x, 3lqw General Method for Designing Self-Assembling Protein Nanomaterials 2013 D Baker, N King, W Sheffler, T Yeates - US Patent App. 13/802,464, 2013 - Google Patents ... subunits. The wild-type protein from which O3-33 was derived (PDB ID 3N79) did not assemble to a higher order structure; it eluted from the column mostly as trimers, with a small peak corresponding to a dimer of trimers. Analytical ...
331 3qdf 3r6o, 3rr6 Crystal structures of Cg1458 reveal a catalytic lid domain and a common catalytic mechanism for the FAH family 2013 R Tingting, G Yanyan, M May, Z Wenjun? - Biochemical Journal, 2013 - biochemj.org ... Source/description, PDB ID, Resolution (?), Sequence identity (%), Aligned residues, Backbone RMSD (?). C. glutamicum/Cg1458, 4DBF, 1.90, ?, ?, ?. 4DBH, 2.00, ?, ?, ?. Mycobacterium marinum M/MMAR-1718, 3QDF, 2.05, 56.73, 245, 1.11. ...
332 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 ...
333 3tmg - Glycine Betaine Recognition through Cation-PI Interactions in Crystal Structures of Glycine Betaine Complexes with C-Ethyl-pyrogallol [4] arene and C-Ethyl-resorcin [4]arene as Receptors 2013 I Fujisawa, K Aoki - Crystals, 2013 - mdpi.com ... 18. Gardberg, A.; Fox, D.; Staker, B.; Stewart, L. Crystal Structure Of Glycine Betaine, L-Proline ABC Transporter, Glycine/Betaine/L-Proline-Binding Protein (ProX) from Borrelia Burgdorferi;PDB (Protein Data Bank): Upton, NY, USA, 2013; No. 3TMG. 19. ...
334 3md7 3urr, 3uw3, 3swo, 3mqd The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment 2013 S Chakraborty, R Venkatramani, BJ Rao… - …, 2013 - ncbi.nlm.nih.gov ... PDB, NRes, NStructures, Specificity. ... based on the 'sequence to structure to function' paradigmis contingent upon the availability of its 3D-structure. The rapidly developing field of nextgeneration sequencing has exacerbated the bottleneck of obtaining structural data using ...
335 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 ...
336 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 ...
337 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 ...
338 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: ...
339 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 ...
340 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 ...
341 3gvi - Rhizobitoxine enhances nodulation by inhibiting ethylene synthesis of bradyrhizobium elkanii from lespedeza species: validation by homology modelling and 2013 R Vijayan, P Palaniappan, SA Tongmin - World J of pharm and , 2013 - wjpps.com ... docking studies with the known inhibitor rhizobitoxine. The crystal structure of protein was taken from the Protein Data Bank (entry PDB code: 3GVI). So, we considered the active site residues predicted from the LIGSITE and CASTp has been used for binding with ...
342 4ed9 - Function and X-Ray crystal structure of Escherichia coli YfdE 2013 EA Mullins, KL Sullivan, TJ Kappock - PloS one, 2013 - dx.plos.org ... the same orientation as Figure 4B. PDB entries are 4hl6 (white), 4ed9 (dark blue), 1p5h (green) [69], 1pt7 (cyan) [24], 3ubm (orange) [25], 1*k7 (yellow) [70], 1*74 (magenta) [71], and 2g04 (pink) [72]. (B) ML phylogram of the ...
343 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 ...
344 3gbz - The N-terminal extension of UBE2E ubiquitin conjugating enzymes limits chain assembly 2013 FR Schumacher, G Wilson, CL Day - Journal of molecular biology, 2013 - Elsevier ... (a) Overlay of the core domain of UBE2E1 (3GBZ) onto the structure of UBE2D2~Ub conjugate (PDB: 3A33). The interaction between ubiquitin from one molecule, shown as a ribbon (teal) and a surface, and the backside of UBE2D2 (teal ribbon) is shown. ...
345 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 ...
346 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. ...
347 3ngj - Characterization and application of a newly synthesized 2-deoxyribose-5-phosphate aldolase 2013 ZY You, ZQ Liu, YG Zheng, YC Shen - Journal of industrial microbiology & Biotechnology, 2013 - Springer ... The crystal structures of DERAs from Entamoeba histolytica (PDB accession NO. 3NGJ) and Thermotoga maritima (PDB accession NO. 3R12) were used as templates. ... 3NGJ, resolution 1.70 A?) and Thermotoga maritima (54.3 % identity; PDB accession no. ...
348 4f3p - Functional Diversity of Tandem Substrate-Binding Domains in ABC Transporters from Pathogenic Bacteria 2013 F Fulyani, GK Schuurman-Wolters, AV Zagar, A Guskov… - Structure, 2013 - Elsevier Supplemental Information ... unliganded liganded 1 42 glnH Escherichia coli Gln v v 1.94 1GGG, 1WDN 0.5 µM (Hsiao, et al., 1996) 2 38 glnH Burkholderia pseudomallei Gln v 2.4 4F3P nd Abendroth J, 2012 ...
349 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 ...
350 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 ...
351 3q1t - Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs) 2013 Z Wang, P Yin, JS Lee, R Parasuram? - BMC Bioinformatics, 2013 - biomedcentral.com ... A structural genomics protein from Mycobacterium avium (PDB ID 3q1t) has been reported to be an enoyl-CoA hydratase (ECH), but SALSA ... There are currently over 11,000 structural genomics (SG) protein structures in the Protein Data Bank (PDB) [1] and most of them are of ...
352 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. ...
353 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. ...
354 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. ...
355 3mc4 - The cysteine regulatory complex from plants and microbes: what was old is new again 2013 JM Jez, S Dey - Current opinion in structural biology, 2013 - Elsevier ... To date, both hexameric and trimeric SAT have been described in the literature [ 12?, 13, 14 and 15 ] and as unpublished structures (PDB: 3GVD, 3MC4, 3F1X). The hexameric SAT are a dimer of trimers associated through a head-to-head orientation of the N-terminal domains. ...
356 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. ...
357 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 ). ...
358 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 ...
359 3r1i - Insilico Characterization and Homology Modeling of Arabitol Dehydrogenase (ArDH) from Candida albican 2013 MW Sarwar, IB Saleem, A Ali, F Abbas - Bioinformation, 2013 - ncbi.nlm.nih.gov … used for multiple sequence alignment of ArDH with other dehydrogenases from Mycobacterium marinum (PDB Id: 3R1I), Candida parapsilosis ...
360 4eqy - Lipid A Biosynthesis of Multidrug-Resistant Pathogens-A Novel Drug Target 2013 CR Lee, J Hun Lee, B Chul Jeong? - Current pharmaceutical design, 2013 - ingentaconnect.com ... (B) Structure of Burkholderia thai- landensis LpxC homotrimer (PDB ID, 4EQY). This structure shows that the catalytic residue (red) and the substrate-binding residues (blue) clustered around the hydrophobic cleft located between adjacent monomers. ...
361 3men - Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives 2013 F Andreoli, A Jorge Moura Barbosa - Current , 2013 - ingentaconnect.com ... Current Pharmaceutical Design, 2013, Vol. 19, No. 4 583 Table 1. Available 3D Structure ofHuman and Bacterial HDACs Class Name Organism PDB ID Ligand Domain Reference ... [262]Bacterial APAH Burkholderia pseudomallei 3MEN Catalytic Domain [263] a PDB ligand ID ...
362 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. ...
363 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. ...
364 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). ...
365 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. ...
366 3qh4 - Lipid Inclusions in Mycobacterial Infections 2013 M Stehr, AA Elamin, M Singh - 2013 - intechopen.com ... Furthermore the three-dimensional structures of the esterases Rv0045c (PDB 3P2M) [78], Rv1847 (PDB 3S4K), and LipW (3QH4) from M. tuberculosis have been determined, but unfortunately it is not known whether these enzymes are involved in TAG hydrolysis. 3.5. ...
367 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). ...
368 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 ...
369 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 ...
370 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, ...
371 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. ...
372 3lls - Crystal structure of hexanoyl-CoA bound to beta-ketoacyl reductase FabG4 of Mycobacterium tuberculosis 2013 D Debajyoti, B Sudipta, R Amlan, B Rupam? - Biochemical Journal, 2013 - biochemj.org ... The structure of the FabG4?NADH complex was determined by molecular replacement in MOLREP [21] using a monomer of the apoFabG4 structure (PDB code 3LLS). ... MtFabG1 (MabA;PDB code 1UZM) and FabG4 (PDB codes 3LLS and 3Q6I) were chosen as the receptor. ...
373 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. ...
374 3iml - Structural and functional characterisation of the methionine adenosyltransferase from Thermococcus kodakarensis 2013 J Schlesier, J Siegrist, S Gerhardt, A Erb? - BMC Structural Biology, 2013 - biomedcentral.com ... for archaeal MATs. The only exception from this observation is the structure of the Burkholderia pseudomallei MAT (PDB-ID 3IML), with a less pronounced torsion of only 35?. Figure 7 Spatial arrangement of MAT monomers. ...
375 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 ...
376 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. ...
377 3obk - Impact of quaternary structure dynamics on allosteric drug discovery 2013 EK Jaffe - Current topics in medicinal chemistry, 2013 - ingentaconnect.com ... Toxoplasma gondii PBGS (PDB id 3OBK, shown left) contains a 13 amino acid C-terminal exten- sion that forms a domain swapped beta sheet (orange/yellow), which locks the dimer into the pro-octamer conformation. Pseudomonas ...
378 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
379 3d64 - S-adenosyl-L-homocysteine hydrolase and methylation disorders: Yeast as a model system 2013 O Tehlivets, N Malanovic, M Visram… - … et Biophysica Acta (BBA …, 2013 - Elsevier ... 1. AdoMet — a principal methyl group donor and more. Beyond its role in protein synthesisand structure, methionine, after its activation to AdoMet by methionine adenosyltransferase,plays a crucial role in many aspects of cellular metabolism. ...
380 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]. ...
381 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, ...
382 3gka - Structural studies of the< i> Trypanosoma cruzi</i> Old Yellow Enzyme: Insights into enzyme dynamics and specificity 2013 MT Murakami, NC Rodrigues, LM Gava? - Biophysical Chemistry, 2013 - Elsevier ... of the TcOYE structure in P2 1 2 1 2 1 and P2 1 crystalline forms have been deposited in the Protein Data Bank with the ... ? rmsd over 348 C? atoms - PDB code: 2GOU) and Burkholderia pseudomallei (BpOYE - 1.24 ? rmsd over 341 C? atoms - PDB code: 3GKA) revealed a ...
383 3fdz - Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation 2013 T Hitosugi, L Zhou, J Fan, S Elf, L Zhang, J Xie? - Nature Communications, 2013 - nature.com ... (a) Cartoon representation of 2,3-BPG location from structure 3FDZ superposed on PGAM1 (PDB accession code: 1YFK). H11 and Y92 are directly proximal to and Y26 is also close to cofactor (2,3-BPG)/substrate (3-PG) binding site. ...
384 3l56 - 3D Molecular Modelling Study of the H7N9 RNA-Dependent RNA Polymerase as an Emerging Pharmacological Target 2013 D Vlachakis, A Karozou, S Kossida - Influenza research and treatment, 2013 - hindawi.com ... The sequence alignment and the blastp query that followed revealed that the PA domain was available in the PDB databank. ... entry: 4ENF), and the crystal structure of the large C-terminal domain of the polymerase basic protein 2 from influenza A virus (RCSB entry: 3L56). ...
385 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) ...
386 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 ...
387 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 ...
388 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
389 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 ...
390 3kre 3r9r Structure of SAICAR synthetase from< i> Pyrococcus horikoshii</i> OT3: Insights into thermal stability 2013 K Manjunath, SP Kanaujia, S Kanagaraj? - International journal of ?, 2012 - Elsevier ... of the native and its complex from S. cerevisiae (PDB-ids: 1obg, 1obd, 2cnu, 2cnv, 2cnq), T. maritima (PDB-id: 1kut; [36]), E. coli (PDB-ids: 2gqs, 2gqr; [37]), G. kaustophilus (PDB-id: 2ywv), M. jannaschii (PDB-ids: 2z02, 2yzl), E. chaffeensis (PDB-id: 3kre), C. perfringens (PDB-id ...
391 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 ...
392 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. ...
393 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 ...
394 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 ...
395 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...
396 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 ...
397 3r20 - Insight from the structural molecular model of cytidylate kinase from Mycobacterium tuberculosis 2013 NK Verma, B Singh - Bioinformation, 2013 - ncbi.nlm.nih.gov ... known structure (template) of Mycobacterium smegmatis (PDB ID: 3R20) was chosen from proteindatabank (PDB) by using ... experimental structure of cytidylate kinase of Mycobacterium tuberculosis is not yet available in PDB (Protein Data Bank), comparative modeling ...
398 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 ...
399 3rr2 - Biochemical properties of nematode< i> O</i>-acetylserine (thiol) lyase paralogs imply their distinct roles in hydrogen sulfide homeostasis 2013 R Vozdek, A Hn?zda, J Krijt, L ?er?, V Ko?ich - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2013 - Elsevier ... First, their amino acid sequences, together with sequences of OAS-TL (PDB ID: 1D6S, 1FCJ, 1O58, 1VE1, 1Y7L, 1Z7W, 2EGU, 2JC3, 2PQM, 2Q3D, 2V03 and 3RR2) and CBS (PDB ID: 1JBQ and 3PC3) were aligned using MUSCLE 3.8.31 [23]. ...
400 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 ...
401 3uam - Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the basidiomycota fungus Phanerochaete chrysosporium 2013 M Wu, GT Beckham, AM Larsson, T Ishida? - Journal of Biological Chemistry, 2013 - ASBMB ... date, there are five LPMO structures from five different fungal GH61s available: H. jecorina GH61B (Protein Data Bank (PDB) code 2VTC ... PDB code 2XWX) (17), Enterococcus faecalis CBM33 (PDB code 4A02) (18), and Burkholderia pseudomallei CBM33 (PDB code 3UAM ...
402 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 ...
403 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). ...
404 3ixc - PIM: Phase Integrated Method for Normal Mode Analysis of Biomolecules in a Crystalline Environment 2013 M Lu, J Ma - Journal of molecular biology, 2013 - Elsevier ... There are totally 29 out of the 65 space groups in this case, shown in the leftmost column of Table 1. In the Protein Data Bank (PDB), 73.3% of the structures belong to this case. ... In the PDB, 24.0% of the structures belong to the case. ...
405 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.
406 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). ...
407 4fry - CBS domains: Ligand binding sites and conformational variability 2013 J Ere?o-Orbea, I Oyenarte, LA Mart?nez-Cruz - Archives of biochemistry and biophysics, 2013 - Elsevier ... At present 120 crystal structures containing 52 different ligands have been reported in the protein data bank (PDB). Of these, 56 entries correspond to eukaryal, 47 to bacterial and 17 to archaeal proteins, respectively. Among ...
408 4iz9 - Mechanistic features of< i> Salmonella typhimurium</i> propionate kinase (TdcD): Insights from kinetic and crystallographic studies 2013 S Chittori, DK Simanshu, S Banerjee? - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2013 - Elsevier ... The recently deposited structure of Mycobacterium avium acetate kinase (PDB ID: 4IZ9; unpublished results) determined in complex with succinic acid–APC (a nucleotide analog) conjugate also shows a bound EDO at the proposed SCFA-II site ( Supplementary Fig. S1) consistent with the conserved nature of ligand binding mechanism in acetokinase family of enzymes ...
409 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. ...
410 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. ...
411 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 ...
412 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 ...
413 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. ...
414 3sdo - Halogen bonding at the ATP binding site of protein kinases: Preferred geometry and topology of ligand binding 2013 J Pozna?ski, D Shugar - Biochimica et Biophysica Acta (BBA)-Proteins and ?, 2013 - Elsevier ... bonding mode occurs to the p-loop region (Arg43-Phe54 in CK2?) in 1 J91, 1ZLT, 2GU8, 2UW8, 2X6D 3NGA 3SDO, frequently accompanying ... Thus, the side-chain carboxyl of Asp (PDB IDs: 1ZOH, 3KXG, 1Q4L, 1FVT, 1UV5, 3ZZ2), a backbone carbonyl of Gly (PDB IDs: 2XP2 ...
415 3h81 4f47, 3rsi, 3r9s, 3r9t, 3oc7 Sequence analysis and structure prediction of enoyl-CoA hydratase from< i> Avicennia marina</i>: Implication of various amino acid residues on substrate–enzyme interactions 2013 U Jabeen, A Salim - Phytochemistry, 2013 - Elsevier ... Appendix A. Supplementary data. ...The second clade has many subdivisions. Enoyl-CoA hydratases in this clade belonged to Bacillus anthracis (3KQF, 3PEA), Geobacillus kaustophilus (2PBP), Mycobacterium tuberculosis (3PZK, 3H81, 3Q0J), Rattus norvegicus (1EY3, 1MJ3, 1DUB, 1DCI), Homo sapiens (2HW5, 2VRE), Escherichia coli K-12 (4FZW), Mycobacterium abscessus (3RSI) ...
416 3cxk - Methionine sulfoxide reduction in ciliates: Characterization of the ready-to-use methionine sulfoxide-< i> R</i>-reductase genes in< i> Euplotes</i> 2013 N Dobri, EEN Oumarou, C Alimenti, C Ortenzi? - Gene, 2012 - Elsevier ... The crystallographic structure of the Burkholderia pseudomallei MsrB (PDB ID: 3cxk) was automatically selected by the server as a template since it shows an amino acid sequence identity of 53% and 56% with the MsrB protein of E. raikovi and E. nobilii, respectively. ...
417 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 ...
418 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). ...
419 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 ...
420 3r1j - Protein Similarity Networks Reveal Relationships among Sequence, Structure, and Function within the Cupin Superfamily 2013 R Uberto, EW Moomaw - PLoS One, 2013 - journals.plos.org File S1 Combined Supporting Information Files - Alpha-ketoglutarate-dependent taurine dioxygenase Mycobacterium avium 3r1j
421 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 ...
422 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. ...
423 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. ...
424 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 ...
425 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 ...
426 3ek1 3i44 Potential monovalent cation-binding sites in aldehyde dehydrogenases 2013 L Gonz?lez-Segura, H Riveros-Rosas? - Chemico-biological Interactions, 2013 - Elsevier ... Cation-binding sites. Family/organism, PDB code, Resolution (?), Monovalent cation in protein solution/crystallization solution, Intra, Inter, Central-cavity a. ... Brucella melitensis, 3EK1, 2.10, nr/(NH 4 ) 2 SO 4 1 M, Proposed (Water ? Na + ), Proposed (Water ? Na + ) i, No (Lys at 479 ...
427 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 ...
428 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). ...
429 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 ...
430 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) ...
431 3p10 - Identification and structural characterization of two 14-3-3 binding sites in the human peptidylarginine deiminase type VI 2012 R Rose, M Rose, C Ottmann - Journal of Structural Biology, 2012 - Elsevier ... of structures ( [Schumacher et al., 2010a], [Schumacher et al., 2010b] and [Molzan et al., 2010]) (PDB IDs: 3NKX, 3O8I, 3IQV, 3LW1, 3IQU, 3IQJ, 3P10, 3P1Q, 3P1N, 3P1R, 3P1S, 3MHR), and which only yields crystals when a peptide is bound in the binding groove of 14-3-3 ?. ...
432 3fs2 - In silico quest for putative drug targets in Helicobacter pylori HPAG1: molecular modeling of candidate enzymes from lipopolysaccharide biosynthesis pathway 2012 M Sarkar, L Maganti, N Ghoshal, C Dutta - Journal of molecular modeling, 2012 - Springer ... Fig. 7 Sequence alignment of 2-dehydro-3-deoxyphosphoocto- nate aldolase of H. pylori HPAG1 with template proteins from Aquifex aeolicus (PDB id: 1fx6), Haemophilus influenza (PDB id: 1o60) and Brucella melitensis (PDB id: 3fs2). ...
433 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), ...
434 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 ...
435 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. ...
436 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 ...
437 3hhj - Insights into substrate recognition by the< i> Escherichia coli</i> Orf135 protein through its solution structure 2012 K Kawasaki, T Kanaba, M Yoneyama? - Biochemical and Biophysical Research Communications, 2012 - Elsevier ... Finally, this study should contribute towards a further understanding of the substrate specificity of Nudix enzymes. For example, the DALI server showed the highest similarity score of 18.9 to the recently published Nudix enzyme (PDB:3hhj) [27]. ...
438 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*. ...
439 3hwi - Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle 2012 A Bagchi - Molecular Biology Reports, 2012 - Springer ... like protein) from Mycobacterium tuberculosis (PDB code: 3HWI) with sequence identity of 34 %. ... The predicted structure is similar to the crystal structure of probable thiosulfate sulfurtransferase Cysa2 (rhodanese-like protein) from Mycobacterium tuberculosis (PDB code: 3HWI). ...
440 3gvg - Crystal structures of triosephosphate isomerase from methicillin resistant< i> Staphylococcus aureus</i> MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop 2012 S Mukherjee, A Roychowdhury, D Dutta, AK Das - Biochimie, 2012 - Elsevier ... Structural homologues to SaTIM in PDB were searched by the BLASTP server [46 ... sequence alignment of amino acid residues of SaTIM (3M9Y) with TIM from Bacillus stearothermophilus (2BTM), Thermotoga maritima (1B9B), Mycobacterium tuberculosis (3GVG), Vibrio marinus ...
441 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]). ...
442 3meq - Asymmetric reduction of diketones by two Gluconobacter oxydans oxidoreductases 2012 P Schweiger, H Gross, J Zeiser? - Applied Microbiology and Biotechnology, 2012 - Springer ... identity, >70 % similarity) to other alcohol dehydrogenase with known 3-D structure, for example, to zinc-dependent alcohol dehydrogenases from Brucella suis (PDB, 3MEQ_A), Pseudomonas ... 2004), 3MEQ from B. suis, and 1RJW from G. stearthermophilus (Ceccarelli et al. ...
443 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. ...
444 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...
445 3py6 - Cation-PI Interactions in beta-Lactamases: The Role in Structural Stability 2012 P Lavanya, S Ramaiah, A Anbarasu - Cell biochemistry and biophysics, 2012 - Springer ... 3PY6-A K37?Y263 -5.33 -1.41 -6.74 K231?W228 -8.02 -1.66 -9.68 2G2W-A R266?F66 -1.62 -1.06 -2.71 R259?W290 -7.01 -4.74 -11.75 K34?W60 -2.81 -0.75 -3.56 Cell Biochem Biophys 123 Page 3. Table 1 continued PDB ID Cation?p interacting residues ...
446 4dz6 - Reflections on biocatalysis involving phosphorus 2012 GM Blackburn, MW Bowler, Y Jin, JP Waltho - Biochemistry (Moscow), 2012 - Springer ... Moreo v er , kindred results can be deriv ed fro m metav ana - date co mplexes, as for the recent structure of a nucleoside diphosphate kinase with ADP linked through v anadate to His134. This show s O–P–N distance of 4.48 Å and an angle of 172.11° (PDB: 4DZ6) ...
447 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 ...
448 3p4i - Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface 2012 S Chittori, H Savithri, M Murthy - BMC structural biology, 2012 - biomedcentral.com ... Crystal structures of two archeal acetate kinases, from Thermotoga maritima (PDB:2IIR, unpublished results) and Methanosarcina thermophila[15] and one from Mycobacterium avium (PDB:3P4I, unpublished results) have been determined earlier. ...
449 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 ...
450 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. ...
451 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. ...
452 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. ...
453 3eoo - Accelerating knowledge-based energy evaluation in protein structure modeling with Graphics Processing Units 2012 A Yaseen, Y Li - Journal of Parallel and Distributed Computing, 2011 - Elsevier ... PDB #of Res #of Atoms GPU Time L1 hits L1 misses Divergent Branches Sorted (??sec) Unsorted (??sec) Sorted/ Unsorted Sorted Unsorted Sorted Unsorted Sorted Unsorted 1PRB 53 419 49 76 ... 1.05 6,88 5 ,7 80 3,83 9 ,5 00 36 4, 04 8 66 6, 21 7 17 9, 78 4 33 ,5 41 3EOO 4,59 ...
454 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 ...
455 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). ...
456 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. ...
457 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. ...
458 3emk 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 ...
459 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 ...
460 3qbp 3rd8, 3rrp Conformational changes upon ligand binding in the essential class II fumarase Rv1098c from< i> Mycobacterium tuberculosis</i> 2012 AE Mechaly, A Haouz, I Miras, N Barilone, P Weber? - FEBS letters, 2012 - Elsevier ... Overall, Rv1098c shows significant structural similarity to deposited structures of mycobacterial homologs (pdb entries 3RD8, 3RRP and 3QBP, all unpublished; Supplementary Table 1), as well as to other members of this superfamily, including aspartases, ?-crystallins ...
461 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. ...
462 3nfw - The C-terminal Domain of 4-Hydroxyphenylacetate 3-Hydroxylase from Acinetobacter baumannii Is an Autoinhibitory Domain 2012 T Phongsak, J Sucharitakul, K Thotsaporn? - Journal of Biological Chemistry, 2012 - ASBMB ... Recently, the structure of the reductase of nitrilotriacetate monooxygenase (NTA_MoB; Protein Data Bank code 3NFW) from Mycobacterium thermoresistibile has been reported (43). However, NTA_MoB (189 residues) is smaller than cB from Chelatobacter sp. (335 residues). ...
463 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. ...
464 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. ...
465 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 ...
466 3uam - Structural Basis for Substrate Targeting and Catalysis by Fungal Polysaccharide Monooxygenases 2012 X Li, WT Beeson, CM Phillips, MA Marletta, JHD Cate - Structure, 2012 - Elsevier ... database (Protein Data Bank [PDB]) contains crystal structures of three CBM33 members, including S. marcescens CBP21 (PDB entry 2BEM) (Vaaje-Kolstad et al., 2005) and two other CBM33s (from Burkholderia pseudomallei and Vibrio cholera, PDB entries 3UAM and 2XWX ...
467 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 ...
468 2kwl - Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction 2012 J Lehtivarjo, K Tuppurainen, T Hassinen? - Journal of biomolecular NMR, 2012 - Springer ... enough. Furthermore, in the static structure of the acyl carrier protein from Borrelia burgdorferi (PDB 2KWL) there are two large 13Ca shift prediction errors (E37Ca, 3.92 ppm and I61Ca, -3.08 ppm) in the loop regions. When ...
469 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 ...
470 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 ...
471 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. ...
472 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). ...
473 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
474 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 ...
475 3obk 3sth, 3ujh Screening for small molecule inhibitors of Toxoplasma gondii 2012 S Kortagere - Expert opinion on drug discovery, 2012 - Taylor & Francis ... A screening for protein targets in T. gondii, for which a crystal structure is available and a ...3OBK Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from T. gondii ME49 in complex with the reaction product porphobilinogenr ...
476 3qh4 3s4k Cytosolic lipid inclusions formed during infection by viral and bacterial pathogens 2012 M Stehr, AA Elamin, M Singh - Microbes and Infection, 2012 - Elsevier ... Furthermore the three-dimensional structures of the esterases Rv0045c (PDB 3P2M) [48], Rv1847 (PDB 3S4K), and LipW (3QH4) from M. tuberculosis have been determined, but unfortunately it is not known whether these enzymes are involved in TAG hydrolysis. 5.5. ...
477 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 ...
478 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 ...
479 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). ...
480 3obk - Allostery and the dynamic oligomerization of porphobilinogen synthase 2012 EK Jaffe, SH Lawrence - Archives of biochemistry and biophysics, 2011 - Elsevier ... B) Subunits B, A and E (corresponding to subunits A,B and F of the oligomers illustrated in part A) of T. gondii PBGS (pdb: 3OBK) are shown as dark teal, gray and light teal cartoons with the remaining subunits of the 8mer shown as transparent white spheres. ...
481 3laa - Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria 2012 MD Hartmann, I Grin? - Proceedings of the ?, 2012 - National Acad Sciences ... was conducted with symmetry constraints; the membrane anchor was modeled by using the Hia membrane anchor domain (PDB ID code ... Comparable interaction patterns can be observed for a HIM2 in the partial Burkholderia pseudomallei TAA head structure 3LAA (17) (Fig. ...
482 3ijp - Enzymology of bacterial lysine biosynthesis 2012 C Dogovski, SC Atkinson? - Biochemistry, Prof. Deniz Ekinci (Ed. ), ISBN: 978-953-51-0076-8, 2012 - cdn.intechopen.com ... 3.2 Structure of DHDPR 3.2.1 Subunit and quaternary structure of DHDPR The three-dimensional structure of DHDPR has been elucidated by X-ray crystallography from five diverse bacterial species, namely, Bartonella henselae, (PDB: 3IJP), E. coli (Scapin et al., 1995, 1997 ...
483 3ijp - Comparative Structure and Function Analyses of Native and His-Tagged forms of Dihydrodipicolinate Reductase from Methicillin-Resistant Staphylococcus aureus 2012 C Dogovski, SR Dommaraju, LC Small? - Protein Expression and Purification, 2012 - Elsevier ... of DHDPR from five bacterial species have been determined by X-ray crystallography, namely from E. coli [25] and [26] (PDB ID: 1ARZ), M. tuberculosis[27] (PDB ID: 1C3V), T. maritima (PDB ID: 1VM6), Bartonella hensalae (PDB ID: 3IJP) and more recently from S. aureus COL ...
484 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). ...
485 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 ...
486 3u03 - Pyoverdine, the Major Siderophore in Pseudomonas aeruginosa, Evades NGAL Recognition 2012 ME Peek, A Bhatnagar, NA McCarty? - Interdisciplinary Perspectives on Infectious Diseases, 2012 - hindawi.com ... Recently, Strong and coworkers crystallized NGAL bound to pyochelin (PDB 3U03, deposited at the RCSB protein data bank) and the crystal structure clearly shows that pyochelin docks inside the calyx of NGAL but without binding avidly. ...
487 3ek2 3k2e, 3grk < i> Staphylococcus aureus</i> FabI: Inhibition, Substrate Recognition, and Potential Implications for In Vivo Essentiality 2012 J Schiebel, A Chang, H Lu, MV Baxter, PJ Tonge? - Structure, 2012 - Elsevier ... bacteria harbor an alanine at this position and, thus, lack the required hydrogen bond acceptor (Figure 3). Consistently, all structurally characterized FabIs from gram-negative organisms contain just a single flexible SBL (PDB codes 2JJY, 2P91, 2WYU, 3EK2, 3GRK, and 3K2E ...
488 3grk - Expression und Mutagenese von VEP1-kodierten Progesteron-5β-Reduktasen aus pharmazeutisch interessanten Angiospermen 2012 P Bauer - 2012 - opus4.kobv.de ... Parallel wurden mit Hilfe der „Superposition“-Funktion der Wincoot Software (II.2.5) in silico die Cosubstrat-Bindetasche der DlP5βR jeweils mit der von verschiedenen NADHabhängigen SDR-Enzymen überlagert (PDB: 2ztl, 3d3w, 3grk,..
489 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 ...
490 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 ...
491 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. ...
492 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 ...
493 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 ...
494 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. ...
495 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 ...
496 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. ...
497 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 ...
498 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. ...
499 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- ...
500 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 ...
501 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 ...
502 3uf8 3vaw A Research on the Use of Voxel Tessellations in the Representation, Investigation and Identification of Protein Surface Atoms and Binding Sites 2012 LL Wei - 2012 - intelligentmodelling.org.uk ... 110 5-13 Visualisations for identified dock site of protein 3UF8 from both RCSB PDB and thevoxel-based method, ... The increasing number of entries being deposited into the Protein DataBank (PDB) ... al, 2007) gives a comprehensive ordering of all proteins of known structure ...
503 3quv - INSILICO CHARACTERIZATION OF TRANSFER RNA (M G37) METHYLTRANSFERASE IN BACTERIA, ARCHAEA AND EUKARYOTA 2011 T Srinivasan, D Sudarsanam - jbstonline.com ... TrmD, aTrm5 and eTrm5 protein was modeled based on the 3QUV-B, 2ZZN-A, and PYX1Ain respectively. ... eTrm5 three dimensional structure is not available in PDB that has distinctlystructural topology to bacterial TrmD. 4. DISCUSSION ...
504 3ftp 3lls, 3grp Crystal structure of FabG4 from< i> Mycobacterium tuberculosis</i> reveals the importance of C-terminal residues in ketoreductase activity 2011 D Dutta, S Bhattacharyya, S Mukherjee, B Saha? - Journal of Structural Biology, 2011 - Elsevier ... to 356 (loop II), and 395 to 417. Domain II is the catalytic domain and share highest sequence homology with Burkholderia Pseudomallei FabG (PDB: 3FTP, 42% in 248 residues overlap). The active site, deep-seated into the ...
505 3krs - Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations 2011 S Yun, HR Guy - Journal of Molecular Graphics and Modelling, 2011 - Elsevier ... patterns and high resolution (less than 2.0 ? resolution) were selected for this study: a human serum retinol-binding protein (RBP with PDB ID 1JYD) [24], a regulator of G-protein signaling (RGS4 with PDB ID 1EZT) [25], and triosephosphate isomerase (TIM with PDB ID 3KRS). ...
506 3lg6 - Identification and clarification of the role of key active site residues in bacterial glutathione< i> S</i>-transferase zeta/maleylpyruvate isomerase 2011 T Fang, DF Li, NY Zhou - Biochemical and Biophysical Research Communications, 2011 - Elsevier ... 2. Phylogenetic relationships of NagL (PDB ID, 2JL4) and other representative cGSTs from the protein data bank. ... delta (1V2A, 1R5A, 3F6F, 3EIN, 1PN9, 1JLV, 3F63 and lJLW), omega (1EEM), tau (2VO4, 1OYJ and 1GWC) and zeta (1FW1, 1E6B, 2JL4, 3NIV, 3LG6 and 2CZ2). ...
507 3ej0 3gqt In silico modeling of cooperative ligand binding 2011 M Vass - theop11.chem.elte.hu ... binding conformations of ligands. A set of 115 X-ray crystal structures was collected from the RCSB Protein Data Bank (PDB) containing at least two non-cofactor type ligands in close proximity to each other believed to be a result of cooperative binding. The commercial ...
508 3emj 3ld3, 3lo0, 3gvf, 3fq3 The Structural Basis for inorganic Pyrophosphatase Catalysis and Regulation 2011 H Tuominen - 2011 - doria.fi ... In addition, the PPase structures from five other species (Anaplasma phagocytophilum, Ehrlichia chaffeensis, Burkholderia pseudomallei, Brucella melitensis and Rickettsia prowazekii) (PDB ID: 3LD3, 3LO0, 3GVF, 3FQ3 and 3EMJ, respectively) obtained in the latest structural ...
509 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 ...
510 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, ...
511 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. ...
512 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 ...
513 3emk - The Crystal Structure of l-Sorbose Reductase from< i> Gluconobacter frateurii</i> Complexed with NADPH and l-Sorbose 2011 K Kubota, K Nagata, M Okai, K Miyazono? - Journal of molecular Biology, 2011 - Elsevier ... Appendix A. ... Strictly conserved residues among the proteins are shown with a red background. Protein names are shown as PDB accession numbers: 2HQ1, glucose/ribitol dehydrogenase from Clostridium thermocellum; 3EMK, glucose/ribitol dehydrogenase from Brucella melitensis; ...
514 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. ...
515 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 ...
516 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 ...
517 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 ...
518 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 ...
519 3oec - Biochemical Studies and Ligand-bound Structures of Biphenyl Dehydrogenase from Pandoraea pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme 2011 S Dhindwal, DN Patil, M Mohammadi? - Journal of Biological Chemistry, 2011 - ASBMB ... PDB code 1BDB and BphB B-356 are shown in black color, and other structures are shown in light colors. These PDB codes are: 2HQ1, 3OEC, 3PKO, 2UVD, 2PNF, 2WSB, 1YDE, 2WDZ, 1HDC, and 1NFR. Reactivity of BphB B-356 with Polychlorinated Biphenyls. ...
520 3md7 - The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold 2011 F Fernandez, F Garces, M L?pez-Estepa? - BMC evolutionary biology, 2011 - biomedcentral.com ... Furthermore, the recently determined structure of a MBL from Brucella melitensis subsp. abortus (PDB ID 3md7 and structures thereof) (unpublished) has revealed a monomeric enzyme with an Mn2+-dependent active site similar to UlaG and in contrast to the Zn2+ ligand found in all other RNases. . ...
521 3l56 - Influence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymerase 2011 A Foeglein, EM Loucaides, M Mura? - Journal of General Virology, 2011 - Soc General Microbiol ... The side chains of residues G590 and Q591 are yellow. (c) Surface electrostatic potential modelling (using Swiss-Prot: red indicates negative charge, blue positive charge) on the 627 domain of PR8 or tPB2 (adapted from PDB 3L56; Yamada et al., 2010). ...
522 3kw3 - The crystal structure of alanine racemase from Streptococcus pneumoniae, a target for structure-based drug design 2011 H Im, ML Sharpe, U Strych, M Davlieva? - BMC Microbiology, 2011 - biomedcentral.com ... of this enzyme from a further six microorganisms have been deposited in the PDB: Bartonella henselae (PDB ID 3KW3), Oenococcus oeni ... are listed in Table 1. Structure factors and final atomic coordinates for AlrSP have been deposited in the Protein Databank (PDB ID: 3S46). ...
523 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. ...
524 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 ...
525 3o0m - Structural Insights into the Novel Diadenosine 5′,5‴-P1,P4-Tetraphosphate Phosphorylase from Mycobacterium tuberculosis H37Rv 2011 S Mori, K Shibayama, JI Wachino, Y Arakawa - Journal of Molecular Biology, 2011 - Elsevier ... Homo sapiens fragile HIT protein [Fhit; Protein Data Bank (PDB) IDs: 6FIT and 1FHI; Z-score = 16.1 and 15.8, respectively], which is a HIT family Ap n A hydrolase; [11] and [12] Zn-bound HIT family protein from Mycobacterium smegmatis (MSMEG5028; PDB ID: 3O0M; Z-score ...
526 2ke0 2l2s, 3k2c, 2ko7 Insights into immunophilin structure and function 2011 C Lucke, M Weiwad - Current medicinal chemistry, 2011 - ingentaconnect.com ... 18, No. 35 L?cke and Weiwad Table 1. List of FKBP Structure Coordinates Available in the RCSB Database name organism UniProtKB residues mutation(s) PDB ID method resolution ligand(s) reference ... FKBP burkholderia pseudomallei Q63J95 1-113 2KE0 NMR SSGCIDa ...
527 3l56 - Molecular mechanisms of transcription and replication of the influenza A virus genome 2011 S Zhang, T Toyoda - Frontiers in Biology, 2011 - Springer ... (b) The electrostatic potential of PB2 3/3 E627 was calculated using the GRASP program. Modified from Fig. 2 of Kuzuhara et al. (2009b). G: PB2 C-terminal NLS. PDB accession number:3L56. Figures were rendered in PyMOL (http://www.pymol.org/). ...
528 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) ...
529 3enk - Highly selective l-threonine 3-dehydrogenase from< i> Cupriavidus necator</i> and its use in determination of l-threonine 2011 T Ueatrongchit, Y Asano - Analytical Biochemistry, 2011 - Elsevier ... BaGluE, UDP-glucose 4-epimerase from Bacillus anthracis (2C20); BpGluE, UDP-glucose 4-epimerase from Burkholderia pseudomallei (3ENK); SvDHT, DTDP-glucose 4,6-dehydratase from Streptomyces venezuelae (1R66); ...
530 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 ...
531 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. ...
532 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 ...
533 3ge4 - Relation between molecular shape and the morphology of self-assembling aggregates: a simulation study 2011 R V?cha, D Frenkel - Biophysical journal, 2011 - Elsevier Supporting Material Figure2.: A cut through the middle of a protein vesicle formed as bilayer of alpha-helices (3GE4 in Protein Database), where alpha-helices are visualised as rods and unstructured loops as wires
534 3la9 - Structure and biology of trimeric autotransporter adhesins 2011 A ?yskowski, JC Leo, A Goldman - Bacterial Adhesion, 2011 - Springer ... The structures are identified by their PDB ID codes where avail- able. ... structure of Haemophilus HiaDB2; (c) 3emi: structure of Haemophilus Hia 307?442 non-adhesive domain; (d) 3emo: structure of transmembrane domain of Haemophilus Hia 973?1098; (e) 3la9: structure of ...
535 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. ...
536 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.
537 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. ...
538 3fs2 3ez4, 3ijp Targeting multiple targets in Pseudomonas aeruginosa PAO1 using flux balance analysis of a reconstructed genome-scale metabolic network 2011 D Perumal, A Samal, KR Sakharkar… - Journal of drug …, 2011 - Taylor & Francis ... 3D structural information of target protein–ligand molecular complexes is a very usefulmethod to identify high-quality drug targets. ... A search against Protein Data Bank (PDB)helped us shortlist targets that had structure available. ...
539 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. ...
540 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). ...
541 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. ...
542 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 ...
543 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 ...
544 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). ...
545 3hwk - Crystal structure of< i> Salmonella typhimurium</i> 2-methylcitrate synthase: Insights on domain movement and substrate specificity 2011 S Chittori, HS Savithri, MRN Murthy - Journal of Structural Biology, 2011 - Elsevier ... In contrast, structural comparison of StPrpC with Mycobacterium tuberculosis GltA1 (MtGltA1; PDB: 3HWK; unpublished results) and Pyrococcus furiosus CS (PfGltA; type-I CS with shorter N-terminal) showed significant similarity in the core structure as well as in the flanking C-terminal extension...
546 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). ...
547 3ijp - Structure and nucleotide specificity of< i> Staphylococcus aureus</i> dihydrodipicolinate reductase (DapB) 2011 TS Girish, V Navratna, B Gopal - FEBS letters, 2011 - Elsevier ... from Escherichia coli, Mycobacterium tuberculosis, Thermotoga maritima and Bartonella henselae have been determined ( [10], [11] and [18]; PDB:1VM6 (Joint Centre for Structural Genomics) and PDB:3IJP (Seattle Structural Genomics Center for Infectious Disease). ...
548 3md0 - Structure-function relationships of the G domain, a canonical switch motif 2011 A Wittinghofer, IR Vetter - Annual review of biochemistry, 2011 - annualreviews.org ... Two structures of putative ArgK proteins have been solved by structural genomics (2www,3md0), which have an ExxG motif instead of DxxG and alpha-helical N- and C-terminal extensions ...
549 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. ...
550 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). ...
551 3dmo 3mpz Crystal structure determination and dynamic studies of< i> Mycobacterium tuberculosis</i> Cytidine deaminase in complex with products 2011 ZA S?nchez-Quitian, LFSM Timmers? - Archives of Biochemistry and Biophysics, 2011 - Elsevier ... Furthermore, in order to verify if these conformations are in agreement with CDA of different organism previously published, we analyzed other 13 CDA structures (PDB access codes: 3IJF, 3MPZ, 1MQ0, 3DMO, 1UX1, 2D30, 1UX0, 1UWZ, 1JTK, 2FR5, 1ZAB, 2FR6, and 3B8F) ...
552 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 ...
553 3cez 3cxk, 3eoo Insights into function, catalytic mechanism, and fold evolution of selenoprotein methionine sulfoxide reductase B1 through structural analysis 2010 FL Aachmann, LS Sal, HY Kim, SM Marino? - Journal of Biological Chemistry, 2010 - ASBMB ... Relative to MsrB1, the crystal structures of MsrBs from N. gonorhoeae (PDB code 1L1D) (8), X. campestris (PDB code 3HCI) (36), B. pseudomallei (PDB code 3CEZ/3CXK), S. pneumoniae (PDB code 3E0M) (31), and B. subtilis (3E0O) (31), as well as the solution structure of B ...
554 3hhj - Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base 2010 T Nakamura, S Meshitsuka, S Kitagawa, N Abe? - Journal of Biological Chemistry, 2010 - ASBMB ... ?, Z = 19.0) and with dGTP (BdRppH-dGTP, 3EF5, rmsd = 1.9 ?, Z = 18.3) (40) and unknown proteins from Bartonella henselae (3HHJ, rmsd = 1.8 ... ray and NMR structures in the ligand-free form and 3.5 ?for 127 C? atoms between structures in the complex form (PDB IDs: 1MUT ...
555 3pme - The binding of β-d-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: A new class of inhibitors 2010 KM Alexacou, AC Tenchiu, ED Chrysina… - Bioorganic & medicinal …, 2010 - Elsevier ... 11. The structural results show that all inhibitors are bound with essentially no disturbance ofthe overall protein structure. ... However, upon binding to the catalytic site compounds 3pBr, 3pCl,3pCF3, 3oOH, 3pOMe and 3pMe trigger a significant shift of the 280s loop with ...
556 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. ...
557 3gaf - Computational analysis of the SAG 13 gene encoding an alcohol dehydrogenase 2010 M Adhikary, S Ganguli, HJ Chakraborty, P Basu et al. - Journal of Pharmaceutical and Biomedical Sciences - jpbms.info ... protein structure to be used as template using BLAST (Basic Local Alignment Search Tool) (1) against PDB (Protein Data Bank). The sequence with maximum identity and less e value was chosen and used as the reference structure for homology modeling. [3GAF, 1AE1 and ...
558 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....
559 3cez - 1 H, 13 C and 15 N resonance assignment of a zinc-binding methionine sulfoxide reductase type-B from the thermophilic archeabacterium Methanothermobacter thermoautotrophicus 2010 M Carella, O Ohlenschl?ger, R Ramachandran? - Biomolecular NMR Assignments, 2010 - Springer ... 2) as predicted from chemical shifts by using TALOS+ (Shen et al. 2009) are in close agreement with the ones present in other known MSRB structures (eg PDB 3HCJ, 3CEZ, 1L1D). The 13Ca and 13Cb chemical shifts suggested (Kornhaber et al. ...
560 3gvg - Triosephosphate isomerase: a highly evolved biocatalyst 2010 RK Wierenga, EG Kapetaniou, R Venkatesan - Cellular and molecular life Sciences, 2010 - Springer ... 1AW2 M. marina No SO4 Dimer 2.65 20.0 21.9 3GVG M. tuberculosis No Dimer 1.55 14.5 16.9 1R2R O. cuniculus No Dimer 1.5 16.1 19.0 ... 3967 Page 8. Table 1 continued pdb code Source Mutant Active site ligand Oligomeric state Resolution (A? ) Rcryst (%) Rfree (%) ...
561 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. ...
562 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)).. ...
563 3ecd 3h7f Structural adaptation of serine hydroxymethyltransferase to low temperatures 2010 A Siglioccolo, F Bossa, S Pascarella - International journal of biological Macromolecules, 2010 - Elsevier ... Table 5. List of representative structures of SHMT currently available in the Protein Data Bank. PDB id Resolution (Å) Biological source 3ECD 1.60 Burkholderia pseudomallei. ...
564 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). ...
565 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. ...
566 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 ...
567 3d5t 3doc 'Cold spots' in protein cold adaptation: Insights from normalized atomic displacement parameters (< i> B'</i>-factors) 2010 A Siglioccolo, R Gerace, S Pascarella - Biophysical chemistry, 2010 - Elsevier ... Growth temperature of the microorganism sources of the selected proteins were taken from thedatabank DSMZ (http://www.dsmz.de/, Deutsche Sammlung von ... Family, Source a, Growth T (?C) b, Pdb ID c, Res. ... Burkholderia pseudomallei, 40, 3D5T, 2.51, 253/328 (77%), 2, 331. ...
568 2kn9 - Metodos Computacionais para o Calculo de Estruturas de Proteinas: Aproximando o Problema Molecular de Geometria de Distancias de Dados de Ressonancia Magnetica Nuclear 2010 PC Nucci - ic.uff.br ... PMGD Problema Molecular de Geometria de Dist?ncias PMGDD Problema Molecular de Geometria de Dist?ncias Discreto BP Branch-And-Prune RMN Resson?ncia Magn?tica NuclearPDB Protein Data Bank pH Potencial Hidrogeni?nico 12 Page 14. Cap??tulo 1 Introdu??ao ...
569 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. ...
570 3dmo - Structural and functional analyses of< i> Mycobacterium tuberculosis Rv3315c</i>-encoded metal-dependent homotetrameric cytidine deaminase 2010 ZA S?nchez-Quitian, CZ Schneider, RG Ducati? - Journal of structural Biology, 2010 - Elsevier ... in the PDB (3IJF). Fig. 7A and B show two views of the canonical homotetrameric structure observed for CDAs from S. cerevisiae (1R5T), B. subtilis (1UX1, 1UWZ, 1UX0, 1JTK), Mus musculus (1ZAB, 2FR5, 2FR6), Bacillus anthracis (2D30), Burkholderia pseudomallei (3DMO), ...
571 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 ...
572 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 ...
573 2ke0 - In silico prediction of binding sites on proteins 2010 S Leis, S Schneider, M Zacharias - Current medicinal chemistry, 2010 - ingentaconnect.com ... 15 Leis et al. Table 3. Protein Test Structures pdb entry molecule state ligand Rmsd (?)b 2ANO E.coli dihydrofolate reductase bound Inh. MS-SH08-17 0 ... 1FKS_2VCD 1FKS based on 2VCD structure homology --- 2.3 1FKS_2KE0 1FKS based on 2KE0 structure homology --- 2.6 ...
574 3gp5 - Structure and Activity of the Metal-independent Fructose-1, 6-bisphosphatase YK23 from Saccharomyces cerevisiae 2010 E Kuznetsova, L Xu, A Singer, G Brown, A Dong? - Journal of Biological Chemistry, 2010 - ASBMB ... of YK23 was solved to 1.75-? resolution using selenomethionine-substituted protein and multiple wavelength anomalous dispersion (PDB code 3F3K ... 2a6p; Z-score 23.7; rms deviation 1.9 ?), the phosphoglyceromutase GpmA from Burkholderia pseudomallei (3gp5; Z-score ...
575 3k9w - Kinetic, Thermodynamic, and Structural Insight into the Mechanism of Phosphopantetheine Adenylyltransferase from< i> Mycobacterium tuberculosis</i> 2010 TJ Wubben, AD Mesecar - Journal of molecular biology, 2010 - Elsevier ... 21 Enteroccoccus faecalis, 22 and Helicobacter pylori; 23 and Staphylococcus aureus in complex with 3'-phosphoadenosine 5'-phosphosulfate, 24 Burkholderia pseudomallei in complex with hydrolyzed dPCoA [Protein Data Bank (PDB) ID 3K9W; unpublished], and ...
576 3fdz - SYSTEM AND USES FOR GENERATING DATABASES OF PROTEIN SECONDARY STRUCTURES INVOLVED IN INTER-CHAIN PROTEIN INTERACTIONS 2010 AL Jochim, PS Arora - US Patent App. 12/753,638, 2010 - Google Patents ... 4, 2010 Sheet 5 of 7 US 2010/0281003 Al EXTRACT PROTEIN STRUCTURES WITH GREATER THAN TWO ENTITIES FROM PDB PROTEIN DATA BANK ASSIGN SECONDARY STRUCTURE ACCORDING TO (() AND vj/ANGLES OF PROTEIN BACKBONE CALCULATE ...
577 3i0p - Helix?helix interactions and their impact on protein motifs and assemblies 2010 N Kurochkina - Journal of Theoretical Biology, 2010 - Elsevier ... Protein, Source, PDB designation. Four-?-helix bundle, Myohemerythrin, Thermiste zostericola, 2 mhr. Hemerythrin, Thermiste discrita, 2hmq. ... Aeropyrum pernix, 2d4a. Entamoeba hystolitica,3i0p. Uridine-diphosphate-galactose 4-epimerase, Trypanosoma brucei, 1gy8. ...
578 3cez 3cxk Methionine sulfoxide reductase B displays a high level of flexibility 2009 FM Ranaivoson, F Neiers, B Kauffmann? - Journal of molecular Biology, 2009 - Elsevier ... View thumbnail images View high quality image (983K). Two X-ray structures of MsrB from Neisseria gonorrhoeae [Protein Data Bank (PDB) ID 1L1D 12 ] and Burkhodelia pseudomallei (PDB IDs 3CXK and 3CEZ; unpublished results) have been determined so far. ...
579 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. ...
580 3eg4 - The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism 2009 L Schuldt, S Weyand, G Kefala, MS Weiss - Journal of molecular biology, 2009 - Elsevier ... coli (PDB entry 3BXY), 7 Campylobacter jejuni (PDB entry 2RIJ, Joint Center for Structural Genomics, unpublished results), Enterococcus faecalis (PDB entry 3CJ8, K. Tan et al., unpublished results) and Brucella melitensis biovar abortus (PDB entry 3EG4, Seattle Structure ...
581 3gwe - Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme 2009 KS Gajiwala, S Margosiak, J Lu, J Cortez, Y Su, Z Nie? - FEBS letters, 2009 - Elsevier ... bacterial species, two of which are Gram-positive organisms (E. faecalis and S. aureus[11]) and five Gram-negative (E. coli[10] and [12], H. influenzae, A. aeolicus (PDB ID: 2EBD), T. thermophilus (PDB ID: 1UB7) and B. pseudomallei (PDB ID: 3GWE)); M. tuberculosis[13] and ...
582 3ecd - Model the Solvent-Excluded Surface of 3D Protein Molecular Structures Using Geometric PDE-Based Level-Set Method 2009 Q Pan, XC Tai - Communications in Computational Physics, 2009 - uib.no ... where ? is a very small value and chosen to be O(?x). 3 Numerical implementation 3.1 Initial construction The data of the complex 3D protein molecular structures, saved as pdb format files, can be downloaded from the free website of the protein data bank: http://www.rcsb.org. ...
583 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 ...
584 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. ...
585 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 ? ...
586 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 ...
587 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. ...