Structure of PDB 4dna Chain B Binding Site BS01

Receptor Information
>4dna Chain B (length=461) Species: 266834 (Sinorhizobium meliloti 1021) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFDYDLFVIGGGSGGVRSGRLAAALGKKVAIAEEFRYGGTCVIRGCVPKK
LYVYASQFAEHFEDAAGFGWTVGESRFDWAKLVAAKEQEIARLEGLYRKG
LANAGAEILDTRAELAGPNTVKLLASGKTVTAERIVIAVGGHPSPHDALP
GHELCITSNEAFDLPALPESILIAGGGYIAVEFANIFHGLGVKTTLIYRG
KEILSRFDQDMRRGLHAAMEEKGIRILCEDIIQSVSADADGRRVATTMKH
GEIVADQVMLALGRMPNTNGLGLEAAGVRTNELGAIIVDAFSRTSTPGIY
ALGDVTDRVQLTPVAIHEAMCFIETEYKNNPTSPDHDLIATAVFSQPEIG
TVGITEEEAARKFQEIEVYRAEFRPMKATLSGRKEKTIMKLVVNAADRKV
VGAHILGHDAGEMAQLLGISLRAGCTKDDFDRTMAVHPTAAEELVTMYQP
SYRVRNGERVG
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 chain4dna Chain B Residue 500 [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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PDB4dna CRYSTAL STRUCTURE OF putative glutathione reductase from Sinorhizobium meliloti 1021
Resolution2.8 Å
Binding residue
(original residue number in PDB)		I11 G12 G14 S15 A34 E35 E36 T42 C43 G47 C48 K51 R114 A115 V141 Y180 I181 R266 G305 D306 Q312 L313 T314
Binding residue
(residue number reindexed from 1)		I9 G10 G12 S13 A32 E33 E34 T40 C41 G45 C46 K49 R112 A113 V139 Y178 I179 R264 G303 D304 Q310 L311 T312
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y39 C43 C48 K51 Y180 E184 A437 H439 E444 G463
Catalytic site (residue number reindexed from 1) Y37 C41 C46 K49 Y178 E182 A435 H437 E442 G461
Enzyme Commision number 1.8.1.7: glutathione-disulfide reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004362 glutathione-disulfide reductase (NADPH) activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0050660 flavin adenine dinucleotide binding
GO:0050661 NADP binding
Biological Process
GO:0006749 glutathione metabolic process
GO:0034599 cellular response to oxidative stress
GO:0045454 cell redox homeostasis
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4dna, PDBe:4dna, PDBj:4dna
PDBsum4dna
PubMed
UniProtQ92PC0

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