› 4gaz

X-ray diffraction
2.81Å resolution

Crystal Structure of a Jumonji Domain-containing Protein JMJD5

Released:
DOI: 10.2210/pdb4gaz/pdb
PDB entry 4gaz coloured by chain, front view.
PDB entry 4gaz coloured by chain, side view.
PDB entry 4gaz coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Wang H, Zhou X, Zhang X, Tao Y, Chen N, Zang J

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 252 amino acids
Theoretical weight: 29.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N371 (Residues: 176-416; Coverage: 58%)
Gene names: JMJD5, KDM8
Sequence domains: Cupin-like domain
Structure domains: Cupin

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P3221
Unit cell:
a: 69.431Å b: 69.431Å c: 270.052Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.221 0.274
Expression system: Escherichia coli

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