Structure of PDB 5v2y Chain A Binding Site BS01

Receptor Information

>5v2y Chain A (length=341) Species: 319 (Pseudomonas savastanoi pv. phaseolicola)

TNLQTFELPTEVTGCAADISLGRALIQAWQKDGIFQIKTDSEQDRKTQEA
MAASKQFCKEPLTFKSSCVSDLTYSGYVASGEEVTAGKPDFPEIFTVCKD
LSVGDQRVKAGWPCHGPVPWPNNTYQKSMKTFMEELGLAGERLLKLTALG
FELPINTFTDLTRDGWHHMRVLRFPPQTSTLSRGIGAHTDYGLLVIAAQD
DVGGLYIRPPVEGEKRNRNWLPGESSAGMFEHDEPWTFVTPTPGVWTVFP
GDILQFMTGGQLLSTPHKVKLNTRERFACAYFHEPNFEASAYPLFEPSAN
ERIHYGEHFTNMFMRCYPDRITTQRINKENRLAHLEDLKKY

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 5v2y Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v2y Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist.
• Resolution: 1.428 Å
• Binding residue (original residue number in PDB): H189 D191 H268
• Binding residue (residue number reindexed from 1): H188 D190 H267
• Annotation score: 1

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

External links

• PDB: RCSB:5v2y, PDBe:5v2y, PDBj:5v2y
• PDBsum: 5v2y
• PubMed: 28780854
• UniProt: P32021|EFE_PSESH 2-oxoglutarate-dependent ethylene/succinate-forming enzyme (Gene Name=efe)