Structure of PDB 8owm Chain D Binding Site BS01
Receptor Information
>8owm Chain D (length=412) Species:
3702
(Arabidopsis thaliana) [
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AMNALAATNRNFRHASRILGLDSKIERSLMIPFREIKVECTIPKDDGTLV
SYIGFRVQHDNARGPMKGGIRYHPEVDPDEVNALAQLMTWKTAVADIPYG
GAKGGIGCSPRDLSLSELERLTRVFTQKIHDLIGIHTDVPAPDMGTNAQT
MAWILDEYSKFHGHSPAVVTGKPIDLGGSLGREAATGRGVVFATEALLAE
YGKSIQGLTFVIQGFGNVGTWAAKLIHEKGGKVVAVSDITGAIRNPEGID
INALIKHKDATGSLNDFNGGDAMNSDELLIHECDVLIPCALGGVLNKENA
GDVKAKFIVEAANHPTDPDADEILSKKGVIILPDIYANAGGVTVSYFEWV
QNIQGFMWEEEKVNLELQKYMTRAFHNIKTMCHTHSCNLRMGAFTLGVNR
VARATQLRGWEA
Ligand information
Ligand ID
NAD
InChI
InChI=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
InChIKey
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
Software
SMILES
CACTVS 3.341
NC(=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 1.5.0
c1cc(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 3.341
NC(=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 1.5.0
c1cc(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
Formula
C21 H27 N7 O14 P2
Name
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBL
CHEMBL1234613
DrugBank
DB14128
ZINC
PDB chain
8owm Chain D Residue 501 [
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Receptor-Ligand Complex Structure
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PDB
8owm
Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site.
Resolution
1.7 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 score
4
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
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:8owm
,
PDBe:8owm
,
PDBj:8owm
PDBsum
8owm
PubMed
37478728
UniProt
Q38946
|DHE2_ARATH Glutamate dehydrogenase 2 (Gene Name=GDH2)
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