Structure of PDB 8owm Chain F Binding Site BS01

Receptor Information
>8owm Chain F (length=412) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMNALAATNRNFRHASRILGLDSKIERSLMIPFREIKVECTIPKDDGTLV
SYIGFRVQHDNARGPMKGGIRYHPEVDPDEVNALAQLMTWKTAVADIPYG
GAKGGIGCSPRDLSLSELERLTRVFTQKIHDLIGIHTDVPAPDMGTNAQT
MAWILDEYSKFHGHSPAVVTGKPIDLGGSLGREAATGRGVVFATEALLAE
YGKSIQGLTFVIQGFGNVGTWAAKLIHEKGGKVVAVSDITGAIRNPEGID
INALIKHKDATGSLNDFNGGDAMNSDELLIHECDVLIPCALGGVLNKENA
GDVKAKFIVEAANHPTDPDADEILSKKGVIILPDIYANAGGVTVSYFEWV
QNIQGFMWEEEKVNLELQKYMTRAFHNIKTMCHTHSCNLRMGAFTLGVNR
VARATQLRGWEA
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 chain8owm Chain F 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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PDB8owm Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		R70 D142 M143 R181 T185 F214 G215 N216 V217 D237 I238 C288 A289 A311 N312 N337
Binding residue
(residue number reindexed from 1)		R71 D143 M144 R182 T186 F215 G216 N217 V218 D238 I239 C289 A290 A312 N313 N338
Annotation score4
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
Cellular Component
GO:0000325 plant-type vacuole
GO:0005739 mitochondrion
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8owm, PDBe:8owm, PDBj:8owm
PDBsum8owm
PubMed37478728
UniProtQ38946|DHE2_ARATH Glutamate dehydrogenase 2 (Gene Name=GDH2)

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