PDBe 4hon

X-ray diffraction
1.8Å resolution

Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate

Released:

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 4D Chains: A, B
Molecule details ›
Chains: A, B
Length: 330 amino acids
Theoretical weight: 38.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6B0I6 (Residues: 12-341; Coverage: 63%)
Gene names: JHDM3D, JMJD2D, KDM4D
Sequence domains:
Structure domains: Cupin
Histone H3.1 Chains: F, G
Molecule details ›
Chains: F, G
Length: 10 amino acids
Theoretical weight: 1.02 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 7-16; 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


1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 72.202Å b: 79.675Å c: 175.938Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.214
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided