› 4qu1

X-ray diffraction
1.57Å resolution

Crystal structure of human JMJD5 jmj-c domain

Released:
DOI: 10.2210/pdb4qu1/pdb
PDB entry 4qu1 coloured by chain, front view.
PDB entry 4qu1 coloured by chain, side view.
PDB entry 4qu1 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Liu HL, Wang C, Zhang GY

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185372 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional peptidase and arginyl-hydroxylase JMJD5 Chain: A
Molecule details ›
Chain: A
Length: 236 amino acids
Theoretical weight: 27.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N371 (Residues: 183-416; Coverage: 56%)
Gene names: JMJD5, KDM8
Sequence domains: Cupin-like domain
Structure domains: Cupin

Ligands and Environments

3 bound ligands:
Ligand NI 1 x NI
Ligand AKG 1 x AKG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 49.627Å b: 65.03Å c: 77.782Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.149 0.174
Expression system: Escherichia coli

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