Structure of PDB 8owm Chain F Binding Site BS02

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 IDU5C
InChIInChI=1S/C5H8O6/c6-3(7)1-2-5(10,11)4(8)9/h10-11H,1-2H2,(H,6,7)(H,8,9)
InChIKeyFFGNAYMZNXXDAW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)CCC(O)(O)C(O)=O
OpenEye OEToolkits 2.0.7C(CC(C(=O)O)(O)O)C(=O)O
FormulaC5 H8 O6
Name2,2-bis(oxidanyl)pentanedioic acid;
2,2-dihydroxyglutarate;
2,2-dihydroxypentanedioic acid
ChEMBL
DrugBank
ZINC
PDB chain8owm Chain F Residue 506 [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)		K66 G68 M87 K90 K102 A140 R181 N312 S344
Binding residue
(residue number reindexed from 1)		K67 G69 M88 K91 K103 A141 R182 N313 S345
Annotation score1
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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