Structure of PDB 6vp4 Chain B Binding Site BS03

Receptor Information
>6vp4 Chain B (length=340) 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
GFELPINTFTDLTRDGWHHMRVLRFPPQTSTLSRGIGAHTDYGLLVIAAQ
DDVGGLYIRPPVEGEKRNRNWLPGESSAGMFEHDEPWTFVTPTPGVWTVF
PGDILQFMTGGQLLSTPHKVKLNTRERFACAYFHEPNFEASAYPLFEPSA
NERIHYGEHFTNMFMRCYPDRITTQRINKENRLAHLEDLK
Ligand information
Ligand IDARG
InChIInChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
InChIKeyODKSFYDXXFIFQN-BYPYZUCNSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC(C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[C@@H](CCCNC(N)=[NH2+])C(O)=O
OpenEye OEToolkits 1.5.0C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[CH](CCCNC(N)=[NH2+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCN\C(=[NH2+])N
FormulaC6 H15 N4 O2
NameARGININE
ChEMBL
DrugBank
ZINC
PDB chain6vp4 Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vp4 An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		E84 T86 R171 H189 D191 Y192 R316 C317
Binding residue
(residue number reindexed from 1)		E84 T86 R171 H189 D191 Y192 R316 C317
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:6vp4, PDBe:6vp4, PDBj:6vp4
PDBsum6vp4
PubMed33522811
UniProtP32021|EFE_PSESH 2-oxoglutarate-dependent ethylene/succinate-forming enzyme (Gene Name=efe)

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