› 6i9n

X-ray diffraction
1.36Å resolution

JmjC domain-containing protein 5 (JMJD5) in complex with Mn and L-2-hydroxyglutarate

Released:
DOI: 10.2210/pdb6i9n/pdb
PDB entry 6i9n coloured by chain, front view.
PDB entry 6i9n coloured by chain, side view.
PDB entry 6i9n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of the 2-oxoglutarate binding site of the circadian rhythm linked oxygenase JMJD5.
Islam MS, Markoulides M, Chowdhury R, Schofield CJ
Sci Rep 12 20680 (2022)
PMID: 36450832

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: 256 amino acids
Theoretical weight: 29.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8N371 (Residues: 183-416; Coverage: 56%)
Gene names: JMJD5, KDM8
Sequence domains: Cupin-like domain

Ligands and Environments

4 bound ligands:
Ligand MN 1 x MN
Ligand S2G 1 x S2G
Ligand TRS 1 x TRS
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 49.642Å b: 64.428Å c: 77.543Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.15 0.159
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Kinetic and inhibition studies on human Jumonji-C (JmjC) domain-containing protein 5.
Tumber et al. (2023)
1 more