Structure of PDB 8ad4 Chain A Binding Site BS02

Receptor Information
>8ad4 Chain A (length=279) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKKWECTVISNDNKATFIKELKLAIPDGESVPFRAGGYIQIEAPAHHVK
YADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNV
RIATPPPNNPNVPPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVF
IGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYVEDFDGLAA
ENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMC
GPPMMNAAVINMLKNLGVEEENILLDDFG
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 chain8ad4 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ad4 Conformational coupling of redox-driven Na + -translocation in Vibrio cholerae NADH:quinone oxidoreductase.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		R229 G282 A283 G284 G310 A311 R312 S340 F354 G379 P380 P381 M382 F406
Binding residue
(residue number reindexed from 1)		R101 G154 A155 G156 G182 A183 R184 S212 F226 G251 P252 P253 M254 F278
Annotation score4
Enzymatic activity
Enzyme Commision number 7.2.1.1: NADH:ubiquinone reductase (Na(+)-transporting).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
GO:0051537 2 iron, 2 sulfur cluster binding
Biological Process
GO:0006814 sodium ion transport
Cellular Component
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:8ad4, PDBe:8ad4, PDBj:8ad4
PDBsum8ad4
PubMed37710014
UniProtA5F5Y4|NQRF_VIBC3 Na(+)-translocating NADH-quinone reductase subunit F (Gene Name=nqrF)

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