Primary Citation PubMed: 9154920
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p3d--Python module for structural bioinformatics.
(2009) BMC Bioinformatics 10
PubMed: 19698094 | PubMedCentral: PMC2744707 | DOI: 10.1186/1471-2105-10-258
As a result, a lot of exceptions in pdb files can be handled without additional precautions, for example: a) Multiple models/structures (NMR, e.g. 7GAT [ 14 ]), b) Alternative side-chain conformers (e... g. 1BPH , [ 15 ]) or alternative main chain tracings (e.g. 1AZZ , [ 16 ]), c) disordered residues (e.g. 1EN2 , (Saul et al. 2000)) and d) non amino acid residues, e.g. DNA (e.g. 7GAT [ 14 ]).
Publication Year: 2009
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors.
(2010) BMC Struct Biol 10
PubMed: 20961427 | PubMedCentral: PMC2974730 | DOI: 10.1186/1472-6807-10-36
Complexes containing BPTI, ecotin and ovomucoid inhibitors correspond respectively to g.8, b.16 and g.68 SCOP subfamilies and are represented, respectively, by 1FY8 (inhibiting rat trypsin), 1AZZ (inh... biting crab collagenase) and 1CHO (inhibiting cattle alpha-chymotrypsin) PDB files.
Table 1 List of all PDB files containing serine protease structures used for structural alignment 01- 1LTO 02- 2FPZ 03- 1NN6 04- 3RP2 05- 1K2I 06- 1EQ9 07- 1GCT 08- 1PYT 09- 1ELT 10- 1M9U 11- 1HNE 12- 1GVK 13- 1BRU 14- 1AGJ 15- 1QTF 16- 1HPG 17- 2O8L 18- 1P3C 19- 2PKA 20- 1GVZ 21- 1LO6 22- 1TON 23- 2FOM 24- 2FP7 25- 1DY9 26- 2SGA 27- 1SGP 28- 1PQ7 29- 1TRN 30- 1HJ9 31- 1HJ8 32- 2F91 33- 1H4W 34- 2A31 35- 1A0J 36- 1OS8 37- 1OP0 38- 1BQY 39- 1C5L 40- 1VR1 41- 2PUX 42- 1H8D 43- 1ETR 44- 1ARB 45- 1Y8T 46- 2SFA 47- 1SOT 48- 2H5C 49- 1NPM 50- 1EP5 51- 1FIW 52- 1DLE 53- 1T32 54- 2BZ6 55- 1BIO 56- 1EUF 57- 1EKB 58- 1IAU 59- 2HLC 60- 1Q3X 61- 1EAX 62- 1FUJ 63- 1MBM 64- 1FON 65- 1RTF 66- 1C5Y 67- 1A7S 68 - 1FY8 69 - 1AZZ 70 - 1CHO The last three PDB IDs (underlined) contain a description of the native complexes of: anionic trypsinogen with BPTI , collagenase with Ecotin and alpha-chymotrypsin with Ovomucoid , respectively.
For the 1AZZ file, containing two chains, only chain A (enzyme) and chain C (inhibitor) were used (the PDB file contains a description of a hetero-dimer).
Publication Year: 2010
Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract.
(2011) BMC Evol Biol 11
PubMed: 21418586 | PubMedCentral: PMC3068966 | DOI: 10.1186/1471-2148-11-72
For AGAP005194 HHpred identified three proteins of known structure as best templates: fire ant chymotrypsin, PDB code: 1eq9 , sequence identity 38%, E-value less than 1.4E -45 [ 79 ], fiddler crab col... agenase, PDB code: 1azz , sequence identity 31%, E-value < 1.4E -45 ) [ 80 ] and crayfish trypsin, PDB code: 2f91 , sequence identity 32%, E-value < 1.4E- -45 ) [ 81 ].
Publication Year: 2011
ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.
(2012) J Chem Inf Model 52
PubMed: 22268964 | PubMedCentral: PMC3287116 | DOI: 10.1021/ci2005687
E (subtilisin fold), we obtain 36 similar proteins, and there are two trypsin-like folds among the “Hot” similar proteins: collagenase ( 1azz .
E) and trypsin ( 1azz .
Publication Year: 2012
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