Structure of PDB 1bdb Chain A Binding Site BS01

Receptor Information
>1bdb Chain A (length=267) Species: 306 (Pseudomonas sp.) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLKGEAVLITGGASGLGRALVDRFVAEGAKVAVLDKSAERLAELETDHG
DNVLGIVGDVRSLEDQKQAASRCVARFGKIDTLIPNAGIWDYSTALVDLP
EESLDAAFDEVFHINVKGYIHAVKACLPALVASRGNVIFTISNAGFYPNG
GGPLYTAAKHAIVGLVRELAFELAPYVRVNGVGSGGINSDLRGPSSLGPL
ADMLKSVLPIGRMPEVEEYTGAYVFFATRGDAAPATGALLNYDGGLGVRG
FFSGAGGNDLLEQLNIH
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain1bdb Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1bdb Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G12 S15 G16 L17 D36 K37 D59 V60 N86 T140 S142 Y155 K159 G185 I187 S189 D190 L191
Binding residue
(residue number reindexed from 1)		G12 S15 G16 L17 D36 K37 D59 V60 N86 T140 S142 Y155 K159 G185 I187 S189 D190 L191
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G16 S142 Y155 K159
Catalytic site (residue number reindexed from 1) G16 S142 Y155 K159
Enzyme Commision number 1.3.1.56: cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016628 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
GO:0018509 cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity
GO:0050664 oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor
Biological Process
GO:0009056 catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:1bdb, PDBe:1bdb, PDBj:1bdb
PDBsum1bdb
PubMed9655331
UniProtP47227|BPHB_PARXL Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (Gene Name=bphB)

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