Structure of PDB 6vp5 Chain A Binding Site BS02

Receptor Information
>6vp5 Chain A (length=335) Species: 319 (Pseudomonas savastanoi pv. phaseolicola) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTNLQTFELPTEVTGCAADISLGRALIQAWQKDGIFQIKTDSEQDRKTQE
AMAASKQFCKEPLTFKSSCVSDLTYSGYVASGEEVTAGKPDFPEIFTVCK
DLSVGDQRVKAGWPCHGPVPWPNNTYQKSMKTFMEELGLAGERLLKLTAL
GFELPINTFTDLTRDGWHHMRVLRFPPQTSTLSRGIGAHTEYGLLVIAAQ
DDVGGLYIRPPVEGEKRNRNWLPGESSAGMFEHDEPWTFVTPTPGVWTVF
PGDILQFMTGGQLLSTPHKVKLNTRERFACAYFHEPNFEASAYPLFEPAN
ERIHYGEHFTNMFMRCYPDRITTQRINKENRLAHL
Ligand information
Ligand IDAKG
InChIInChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKeyKPGXRSRHYNQIFN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385OC(=O)CCC(=O)C(O)=O
FormulaC5 H6 O5
Name2-OXOGLUTARIC ACID
ChEMBLCHEMBL1686
DrugBankDB08845
ZINCZINC000001532519
PDB chain6vp5 Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vp5 An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		R171 L173 F175 H189 E191 H268 V270 R277 A279
Binding residue
(residue number reindexed from 1)		R171 L173 F175 H189 E191 H268 V270 R277 A279
Annotation score5
Enzymatic activity
Enzyme Commision number 1.13.12.19: 2-oxoglutarate dioxygenase (ethylene-forming).
1.14.20.7: 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate- forming).
Gene Ontology
Molecular Function
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0102276 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity
Biological Process
GO:0009693 ethylene biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vp5, PDBe:6vp5, PDBj:6vp5
PDBsum6vp5
PubMed33522811
UniProtP32021|EFE_PSESH 2-oxoglutarate-dependent ethylene/succinate-forming enzyme (Gene Name=efe)

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