Structure of PDB 8ad0 Chain B Binding Site BS02

Receptor Information
>8ad0 Chain B (length=384) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATLFYTPGLVTKRSSHVRDSVDLKRIMIMVWLAVFPAMFWGMYNAGGQAI
AALNHLYSGDQLAAIVAGNWHYWLTEMLGGTMSSDAGWGSKMLLGATYFL
PIYATVFIVGGFWEVLFCMVRKHEVNEGFFVTSILFALIVPPTLPLWQAA
LGITFGVVVAKEVFGGTGRNFLNPALAGRAFLFFAYPAQISGDLVWTAAD
GYSGATALSQWAQGGAGALINNATGQTITWMDAFIGNIPGSIGEVSTLAL
MIGAAFIVYMGIASWRIIGGVMIGMILLSTLFNVIGSDTNAMFNMPWHWH
LVLGGFAFGMFFMATDPVSASFTNSGKWAYGILIGVMCVLIRVVNPAYPE
GMMLAILFANLFAPLFDHVVVERNIKRRLARYGK
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 chain8ad0 Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ad0 X-ray structure of Na+-NQR from Vibrio cholerae at 3.4 A resolution
Resolution3.11 Å
Binding residue
(original residue number in PDB)
V60 V161 T162 L165 N200 N203 P204 A205 I292 F342 M343 D346 P347 V348
Binding residue
(residue number reindexed from 1)
V30 V131 T132 L135 N170 N173 P174 A175 I262 F312 M313 D316 P317 V318
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8ad0, PDBe:8ad0, PDBj:8ad0
PDBsum8ad0
PubMed
UniProtA5F5X0|NQRB_VIBC3 Na(+)-translocating NADH-quinone reductase subunit B (Gene Name=nqrB)

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