3dxt

X-ray diffraction
1.8Å resolution

Crystal structure of the catalytic core domain of JMJD2D

Released:
Source organism: Homo sapiens
Entry authors: Chen Z, Zhang G

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

Assemblies composition:
monomeric (preferred)
homo dimer
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4D Chain: A
Molecule details ›
Chain: A
Length: 354 amino acids
Theoretical weight: 40.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6B0I6 (Residues: 1-354; Coverage: 68%)
Gene names: JHDM3D, JMJD2D, KDM4D
Sequence domains:
Structure domains: Cupin

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P43212
Unit cell:
a: 71.63Å b: 71.63Å c: 151.295Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.203
Expression system: Escherichia coli