› 4aap

X-ray diffraction
2.6Å resolution

Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG)

Released:
DOI: 10.2210/pdb4aap/pdb
PDB entry 4aap coloured by chain, front view.
PDB entry 4aap coloured by chain, side view.
PDB entry 4aap coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Vollmar M, Johansson C, Krojer T, Canning P, Allerston C, Gadhave A, von Delft F, Bountra C, Arrowsmith CH, Weigelt J, Edwards A, Oppermann U

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: 239 amino acids
Theoretical weight: 27.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8N371 (Residues: 180-416; Coverage: 57%)
Gene names: JMJD5, KDM8
Sequence domains: Cupin-like domain
Structure domains: Cupin

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand OGA 2 x OGA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P3221
Unit cell:
a: 68.575Å b: 68.575Å c: 269.003Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.208 0.253
Expression system: Escherichia coli BL21(DE3)

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