› 5a1l

X-ray diffraction
2Å resolution

Crystal structure of JmjC domain of human histone demethylase UTY with S21056a

Released:
DOI: 10.2210/pdb5a1l/pdb
PDB entry 5a1l coloured by chain, front view.
PDB entry 5a1l coloured by chain, side view.
PDB entry 5a1l coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Srikannathasan V, Gileadi C, Johansson C, Krojer T, Tumber A, von Delft F, Arrowsmith CH, Bountra C, Edwards A, Brennan P, Oppermann U

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(27) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(27) + succinate + formaldehyde + 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-127019 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone demethylase UTY Chains: A, B
Molecule details ›
Chains: A, B
Length: 478 amino acids
Theoretical weight: 55.01 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O14607 (Residues: 878-1347; Coverage: 35%)
Gene names: KDM6C, UTY
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand FE2 2 x FE2
Ligand S2I 2 x S2I
Ligand EDO 11 x EDO
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 90.711Å b: 110.5Å c: 119.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.225
Expression system: Spodoptera frugiperda

Quick links