Structure of PDB 1nm5 Chain B Binding Site BS01

Receptor Information
>1nm5 Chain B (length=358) Species: 1085 (Rhodospirillum rubrum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIAIPKERRPGEDRVAISPEVVKKLVGLGFEVIVEQGAGVGASITDDAL
TAAGATIASTAAQALSQADVVWKVQRPMTAEEGTDEVALIKEGAVLMCHL
GALTNRPVVEALTKRKITAYAMELMPRISRANSMDILSSQSNLAGYRAVI
DGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMA
TDVRAATKEQVESLGGKFITVEFRKKQAEAVLKELVKTDIAITTALIPGK
PAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGH
TNVPSRVAADASPLFAKNLLNFLTPHVDKDTKTLVMKLEDETVSGTCVTR
DGAIVHPA
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/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/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[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 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[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
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain1nm5 Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1nm5 Glutamine 132 in the NAD(H)-binding component of proton-translocating transhydrogenase tethers the nucleotides before hydride transfer.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G181 V182 D202 V203 R204 L275
Binding residue
(residue number reindexed from 1)		G181 V182 D202 V203 R204 L255
Annotation score4
Binding affinityMOAD: Kd=20uM
Enzymatic activity
Catalytic site (original residue number in PDB) R15 Q75 H99 G101 E123 R127 N132 D135 S138 E296
Catalytic site (residue number reindexed from 1) R15 Q75 H99 G101 E123 R127 N132 D135 S138 E276
Enzyme Commision number 7.1.1.1: proton-translocating NAD(P)(+) transhydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003957 NAD(P)+ transhydrogenase (Si-specific) activity
GO:0005515 protein binding
GO:0008750 proton-translocating NAD(P)+ transhydrogenase activity
GO:0016491 oxidoreductase activity
GO:0046983 protein dimerization activity
GO:0050661 NADP binding
GO:0051287 NAD binding
GO:0070403 NAD+ binding
GO:0070404 NADH binding
Biological Process
GO:0006740 NADPH regeneration
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1nm5, PDBe:1nm5, PDBj:1nm5
PDBsum1nm5
PubMed12564924
UniProtQ2RSB2|PNTAA_RHORT NAD(P) transhydrogenase subunit alpha part 1 (Gene Name=pntAA)

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