Structure of PDB 7xk3 Chain B Binding Site BS01

Receptor Information
>7xk3 Chain B (length=387) Species: 345073 (Vibrio cholerae O395) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YEAAATLFYTPGLVTKRSSHVRDSVDLKRIMIMVWLAVFPAMFWGMYNAG
GQAIAALNHLYSGDQLAAIVAGNWHYWLTEMLGGTMSSDAGWGSKMLLGA
TYFLPIYATVFIVGGFWEVLFCMVRKHEVNEGFFVTSILFALIVPPTLPL
WQAALGITFGVVVAKEVFGGTGRNFLNPALAGRAFLFFAYPAQISGDLVW
TAADGYSGATALSQWAQGGAGALINNATGQTITWMDAFIGNIPGSIGEVS
TLALMIGAAFIVYMGIASWRIIGGVMIGMILLSTLFNVIGSDTNAMFNMP
WHWHLVLGGFAFGMFFMATDPVSASFTNSGKWAYGILIGVMCVLIRVVNP
AYPEGMMLAILFANLFAPLFDHVVVERNIKRRLARYG
Ligand information
Ligand IDFMN
InChIInChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain7xk3 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7xk3 Cryo-EM structures of Na + -pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		R209 F213 W226 T236 S271 E274 P379 E380 G381 M383
Binding residue
(residue number reindexed from 1)		R183 F187 W200 T210 S245 E248 P353 E354 G355 M357
Annotation score1
Enzymatic activity
Enzyme Commision number 7.2.1.1: NADH:ubiquinone reductase (Na(+)-transporting).
Gene Ontology
Molecular Function
GO:0010181 FMN binding
GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
GO:1902444 riboflavin binding
Biological Process
GO:0006814 sodium ion transport
GO:0022904 respiratory electron transport chain
GO:0055085 transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7xk3, PDBe:7xk3, PDBj:7xk3
PDBsum7xk3
PubMed35882843
UniProtA5F5X0|NQRB_VIBC3 Na(+)-translocating NADH-quinone reductase subunit B (Gene Name=nqrB)

[Back to BioLiP]