Primary Citation PubMed: 12767218
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A novel 9-bp insertion detected in steroid 21-hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods.
(2009) J Biomed Sci 16
PubMed: 19272182 | PubMedCentral: PMC2653521 | DOI: 10.1186/1423-0127-16-3
Assessment of the theoretical structure available for human P450c21 The theoretical structure of human P450c21 (PDB ID: 2GEG ) has been elucidated using rabbit P4502c5 (PDB ID: 1N6B ) as template [ 29... ].
A theoretical structure of human P450c21 (PDB ID: 2GEG ) has been elucidated using rabbit P4502c5 (PDB ID: 1N6B ) as template [ 29 ].
WT represents theoretical structure for human P450c21 (PDB ID: 2GEG ) and the template denotes rabbit P4502c5 (PDB ID: 1N6B ).
Sequence alignment of P4502c5 of rabbit (1DT6/1N6B) with human P450c21 generated by FUGUE server, along with their secondary structure information .
Publication Year: 2009
Prediction and analysis of the modular structure of cytochrome P450 monooxygenases.
(2010) BMC Struct Biol 10
PubMed: 20950472 | PubMedCentral: PMC3224734 | DOI: 10.1186/1472-6807-10-34
Table 2 Positions which correspond to F87 in P450 BM-3 and predicted position, and prediction of positions in new structures CYP PDB-Code Position in crystal structure Predicted position 8A 2IAG - - 5... B1 1E9X - V88 55A2 1CL6 V87 V87 101D 2CPP T101 I99 107A1 1OXA G91 G91 107L1 2BVJ L93 L93 108A 1CPT T103 T103 119 1IO7 L69 L69 152A1 1IZO Q85 Q85 154A1 1ODO F88 F88 154C1 1GWI L93 L93 158A1 2DKK A97 S95 158A2 1S1F G94 G94 165B3 1LFK M89 N87 165C4 1UED S98 S98 167A1 1Q5D F96 G94 175A1 1N97 L80 L80 176A1 1T2B A91 M89 199A2 2FR7 L100 L100 245A1 2Z3T V99 V99 1A2 2HI4 T124 S126 2A6 1Z10 V117 V117 2A13 2P85 A117 A117 2B4 1SUO I114 I114 2C5 1N6B A113 A113 2C8 1PQ2 I113 I113 2C9 1OG2 V113 V113 2D6 2F9Q F120 F120 2R1 2OJD L125 L125 3A4 1TQN S119 S119 102A1 1BU7 (reference) F87 F87 2E1 3E4E I94 I94 3A43 2V0M S119 S119 7A1 2DAX - D98 19A1 3EQM F134 F134 46A1 2Q9F V126 S127 74A1 2RCH S128 L127 105A1 2ZBX I96 I96 105K1 2Z36 L96 L96 120A1 2VE3 A94 A94 231A2 2RFB I48 I48 248A 3BUJ L80 L80 To validate our structure-based method to assign SCRs in a one-leave-out cross-validation, the position which corresponds to F87 in CYP102A1 was predicted for each sequence of each structure.
CYP PDB entry Resolution [Å] Ligand Organism Class II CYPs (CPR-type) 1A2 2HI4 1.95 + Homo sapiens 2A6 1Z10 1.90 + Homo sapiens 2A13 2P85 2.35 + Homo sapiens 2B4 1SUO 1.90 + Oryctolagus cuniculus 2C5 1N6B 2.30 + Oryctolagus cuniculus 2C8 1PQ2 2.70 + Homo sapiens 2C9 1OG2 2.60 + Homo sapiens 2D6 2F9Q 3.00 - Homo sapiens 2R1 2OJD 2.80 + Homo sapiens 3A4 1TQN 2.05 - Homo sapiens 102A1 1BU7 1.65 - Bacillus megaterium (P450 BM-3) 175A1 1N97 1.80 - Thermus thermophilus Class I CYPs 51B1 1E9X 2.10 + Mycobacterium tuberculosis 101D 2CPP 1.63 + Pseudomonas putida (P450cam) 107A1 1OXA 2.10 + Saccharopolyspora erythrea 107L1 2BVJ 2.10 - Streptomyces venezuelae 108A 1CPT 2.30 - Pseudomonas sp .
Publication Year: 2010
Automating crystallographic structure solution and refinement of protein-ligand complexes.
(2014) Acta Crystallogr D Biol Crystallogr 70
PubMed: 24419387 | PubMedCentral: PMC3919266 | DOI: 10.1107/S139900471302748X
In PDB entry 1r9o , for instance, the search model (PDB entry 1n6b ) has only 76% sequence identity and although ligand placement was successful, there are large regions on the surface of the protein ... hat have undergone significant conformational changes and require rebuilding or deletion.
Publication Year: 2014
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