Structure of PDB 7xk5 Chain B Binding Site BS02

Receptor Information
>7xk5 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 IDRBF
InChIInChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1
InChIKeyAUNGANRZJHBGPY-SCRDCRAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO)c2cc1C
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO)O)O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)CO
FormulaC17 H20 N4 O6
NameRIBOFLAVIN;
RIBOFLAVINE;
VITAMIN B2
ChEMBLCHEMBL1534
DrugBankDB00140
ZINCZINC000002036848
PDB chain7xk5 Chain B Residue 502 [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]
PDB7xk5 Cryo-EM structures of Na + -pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
T162 L165 N200 N203 P204 A205 F342 M343 D346 P347 V348
Binding residue
(residue number reindexed from 1)
T136 L139 N174 N177 P178 A179 F316 M317 D320 P321 V322
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:7xk5, PDBe:7xk5, PDBj:7xk5
PDBsum7xk5
PubMed35882843
UniProtA5F5X0|NQRB_VIBC3 Na(+)-translocating NADH-quinone reductase subunit B (Gene Name=nqrB)

[Back to BioLiP]