› 5fy7

X-ray diffraction
1.86Å resolution

Crystal structure of JmjC domain of human histone demethylase UTY in complex with succinate

Released:
DOI: 10.2210/pdb5fy7/pdb
PDB entry 5fy7 coloured by chain, front view.
PDB entry 5fy7 coloured by chain, side view.
PDB entry 5fy7 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Nowak R, Krojer T, Johansson C, Gileadi C, Kupinska K, von Delft F, Arrowsmith CH, Bountra C, Edwards A, 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 MN 2 x MN
Ligand SIN 2 x SIN
Ligand EDO 16 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: 91.69Å b: 110.77Å c: 119.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.225
Expression system: Spodoptera frugiperda

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