Structure of PDB 5vka Chain A Binding Site BS02

Receptor Information
>5vka Chain A (length=348) Species: 319 (Pseudomonas savastanoi pv. phaseolicola) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLQTFELPTEVTGCAADISLGRALIQAWQKDGIFQIKTDSEQDRKTQEAM
AASKQFCKEPLTFKSSCVSDLTYSGYVASGEEVTAGKPDFPEIFTVCKDL
SVGDQRVKAGWPCHGPVPWPNNTYQKSMKTFMEELGLAGERLLKLTALGF
ELPINTFTDLTRDGWHHMRVLRFPPQTSTLSRGIGAHTDYGLLVIAAQDD
VGGLYIRPPVEGEKRNRNWLPGESSAGMFEHDEPWTFVTPTPGVWTVFPG
DILQFMTGGQLLSTPHKVKLNTRERFACAYFHEPNFEASAYPLFEPSANE
RIHYGEHFTNMFMRCYPDRITTQRINKENRLAHLEDLKKYSDTRATGS
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 chain5vka 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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PDB5vka Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist.
Resolution1.169 Å
Binding residue
(original residue number in PDB)		R171 L173 F175 H189 D191 H268 V270 R277 A279
Binding residue
(residue number reindexed from 1)		R169 L171 F173 H187 D189 H266 V268 R275 A277
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:5vka, PDBe:5vka, PDBj:5vka
PDBsum5vka
PubMed28780854
UniProtP32021|EFE_PSESH 2-oxoglutarate-dependent ethylene/succinate-forming enzyme (Gene Name=efe)

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