Structure of PDB 6yei Chain A Binding Site BS01

Receptor Information
>6yei Chain A (length=409) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NALAATNRNFKLAARLLGLDSKLEKSLLIPFREIKVECTIPKDDGTLASF
VGFRVQHDNARGPMKGGIRYHPEVDPDEVNALAQLMTWKTAVAKIPYGGA
KGGIGCDPSKLSISELERLTRVFTQKIHDLIGIHTDVPAPDMGTGPQTMA
WILDEYSKFHGYSPAVVTGKPIDLGGSLGRDAATGRGVMFGTEALLNEHG
KTISGQRFVIQGFGNVGSWAAKLISEKGGKIVAVSDITGAIKNKDGIDIP
ALLKHTKEHRGVKGFDGADPIDPNSILVEDCDILVPAALGGVINRENANE
IKAKFIIEAANHPTDPDADEILSKKGVVILPDIYANSGGVTVSYFEWVQN
IQGFMWEEEKVNDELKTYMTRSFKDLKEMCKTHSCDLRMGAFTLGVNRVA
QATILRGWG
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 chain6yei Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6yei Structural Studies of Glutamate Dehydrogenase (Isoform 1) FromArabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism.
Resolution2.02 Å
Binding residue
(original residue number in PDB)		T185 F214 G215 N216 V217 D237 I238 A289 L290 A311 N312 N337
Binding residue
(residue number reindexed from 1)		T184 F213 G214 N215 V216 D236 I237 A288 L289 A310 N311 N336
Annotation score4
Binding affinityMOAD: Kd=72uM
Enzymatic activity
Enzyme Commision number 1.4.1.3: glutamate dehydrogenase [NAD(P)(+)].
Gene Ontology
Molecular Function
GO:0004352 glutamate dehydrogenase (NAD+) activity
GO:0004353 glutamate dehydrogenase [NAD(P)+] activity
GO:0004354 glutamate dehydrogenase (NADP+) activity
GO:0005507 copper ion binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0016639 oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
GO:0050897 cobalt ion binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0009646 response to absence of light
Cellular Component
GO:0005739 mitochondrion
GO:0009536 plastid

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6yei, PDBe:6yei, PDBj:6yei
PDBsum6yei
PubMed32655590
UniProtQ43314|DHE1_ARATH Glutamate dehydrogenase 1 (Gene Name=GDH1)

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