PDBe 5d6y

X-ray diffraction
2.29Å resolution

Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3

Released:

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 4A Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 121 amino acids
Theoretical weight: 13.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75164 (Residues: 895-1011; Coverage: 11%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains: Jumonji domain-containing protein 2A Tudor domain
Structure domains:
Histone H3.1 Chains: a, b, c, d
Molecule details ›
Chains: a, b, c, d
Length: 10 amino acids
Theoretical weight: 1.12 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 20-29; Coverage: 7%)
Gene names: H3FA, H3FB, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

No bound ligands

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P32
Unit cell:
a: 106.159Å b: 106.159Å c: 79.206Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.265 0.264 0.295
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided