› 2xdp

X-ray diffraction
1.56Å resolution

Crystal structure of the tudor domain of human JMJD2C

Released:
DOI: 10.2210/pdb2xdp/pdb
PDB entry 2xdp coloured by chain, front view.
PDB entry 2xdp coloured by chain, side view.
PDB entry 2xdp coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Yue WW, Gileadi C, Krojer T, Weisbach H, Ugochukwu E, Daniel M, Phillips C, Chaikuad A, von Delft F, Allerston C, Arrowsmith C, Weigelt J, Edwards A, Bountra C, Oppermann U

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190587 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4C Chain: A
Molecule details ›
Chain: A
Length: 123 amino acids
Theoretical weight: 14.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H3R0 (Residues: 875-995; Coverage: 12%)
Gene names: GASC1, JHDM3C, JMJD2C, KDM4C, KIAA0780
Sequence domains: Jumonji domain-containing protein 2A Tudor domain
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: I222
Unit cell:
a: 52.815Å b: 79.646Å c: 81.614Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.186 0.206
Expression system: Escherichia coli BL21(DE3)

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