Structure of PDB 6m3s Chain A Binding Site BS01

Receptor Information
>6m3s Chain A (length=333) Species: 339 (Xanthomonas campestris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTITVIRGDGIGPEIMDATLFVLDALQAGLTYEYADAGLVALEKHGDLLP
ESTLASITKNKVALKSPLTTPVGEGFSSINVAMRRKFDLYANVRPAKSFP
NTKSRFADGVDLITVRENTEGAYLSEGQEVSADGEVAVSGARVTRKGSER
IVRYAFDLARATGRKKVTAVHKANIIKSTSGLFLKVARDVATQYPEIEFQ
EMIVDNTCMQLVMRPEQFDIIVTTNLFGDIISDLCAGLVGGLGLAPGANI
GVDAAIFEAVHGSAPDIAGQGKANPCALLLGAAQMLDHIGQPQNAERLRE
AIVATLEAKDSLTPDLGGTGNTMGFAKAIASRL
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 chain6m3s Chain A Residue 401 [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]
PDB6m3s Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004
Resolution2.3 Å
Binding residue
(original residue number in PDB)		P69 L70 T72 N82 L244 E260 H263 G264 S265 A266 D268 N276
Binding residue
(residue number reindexed from 1)		P67 L68 T70 N80 L242 E258 H261 G262 S263 A264 D266 N274
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y125 K174 D207 D231
Catalytic site (residue number reindexed from 1) Y123 K172 D205 D229
Enzyme Commision number 1.1.1.41: isocitrate dehydrogenase (NAD(+)).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004449 isocitrate dehydrogenase (NAD+) activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
Biological Process
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6m3s, PDBe:6m3s, PDBj:6m3s
PDBsum6m3s
PubMed
UniProtA0A0H2XBX7

[Back to BioLiP]