Structure of PDB 6vw7 Chain B Binding Site BS03

Receptor Information
>6vw7 Chain B (length=512) Species: 106590 (Cupriavidus necator) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ITITTIFVPRDSTALALGADDVARAIAREAAARNEHVRIVRNGSRGMFWL
EPLVEVQTGAGRVAYGPVSAADVPGLFDAGLLQGGEHALSQGVTEEIPFL
KQQERLTFARVGITDPLSLDDYRAHEGFAGLERALAMQPAEIVQEVTDSG
LRGRGGAAFPTGIKWKTVLGAQSAVKYIVCNADEGDSGTFSDRMVMEDDP
FMLIEGMTIAALAVGAEQGYIYCRSEYPHAIAVLESAIGIANAAGWLGDD
IRGSGKRFHLEVRKGAGAYVCGEETALLESLEGRRGVVRAKPPLPALQGL
FGKPTVINNVISLATVPVILARGAQYYRDYGMGRSRGTLPFQLAGNIKQG
GLVEKAFGVTLRELLVDYGGGTRSGRAIRAVQVGGPLGAYLPESRFDVPL
DYEAYAAFGGVVGHGGIVVFDETVDMAKQARYAMEFCAIESCGKCTPCRI
GSTRGVEVMDRIIAGEQPVKHVALVRDLCDTMLNGSLCAMGGMTPYPVLS
ALNEFPEDFGLA
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/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/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain6vw7 Chain B Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vw7 Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG fromCupriavidus necator.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		A158 F160 K165 T168 E275 K292 L295
Binding residue
(residue number reindexed from 1)		A157 F159 K164 T167 E274 K291 L294
Annotation score4
Binding affinityMOAD: Kd=190uM
Enzymatic activity
Enzyme Commision number 1.2.1.2: Transferred entry: 1.17.1.9.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:1902600 proton transmembrane transport

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vw7, PDBe:6vw7, PDBj:6vw7
PDBsum6vw7
PubMed32249211
UniProtQ0KDY2

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