Structure of PDB 2yvf Chain A Binding Site BS01

Receptor Information
>2yvf Chain A (length=401) Species: 306 (Pseudomonas sp.) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDF
MAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTL
VLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGV
IGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLR
FERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGI
FVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHL
VDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLI
ELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAA
V
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain2yvf Chain A Residue 1449 [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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PDB2yvf Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin
Resolution1.6 Å
Binding residue
(original residue number in PDB)		G16 A18 D40 R48 P49 A82 T109 G110 L129 R130 I156 E159 G272 D273 T290 W291 A294 W320
Binding residue
(residue number reindexed from 1)		G11 A13 D35 R43 P44 A77 T104 G105 L124 R125 I151 E154 G267 D268 T285 W286 A289 W315
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) L17 R48 P49 Q295
Catalytic site (residue number reindexed from 1) L12 R43 P44 Q290
Enzyme Commision number 1.18.1.2: ferredoxin--NADP(+) reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0016651 oxidoreductase activity, acting on NAD(P)H
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:2yvf, PDBe:2yvf, PDBj:2yvf
PDBsum2yvf
PubMed17850818
UniProtQ52437

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