› 3uyj

X-ray diffraction
2.35Å resolution

Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG

Released:
DOI: 10.2210/pdb3uyj/pdb
PDB entry 3uyj coloured by chain, front view.
PDB entry 3uyj coloured by chain, side view.
PDB entry 3uyj coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Su X, Li H

Function and Biology Details

Reaction catalysed: 
[Protein]-L-arginine + 2-oxoglutarate + O(2) = [protein]-(3R)-3-hydroxy-L-arginine + succinate + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185373 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional peptidase and arginyl-hydroxylase JMJD5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 248 amino acids
Theoretical weight: 28.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N371 (Residues: 173-416; Coverage: 59%)
Gene names: JMJD5, KDM8
Sequence domains: Cupin-like domain
Structure domains: Cupin

Ligands and Environments

2 bound ligands:
Ligand NI 2 x NI
Ligand AKG 2 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P3221
Unit cell:
a: 68.393Å b: 68.393Å c: 266.686Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.203 0.253
Expression system: Escherichia coli

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