› 3dxu

X-ray diffraction
2.2Å resolution

The crystal structure of core JMJD2D complexed with FE and N-oxalylglycine

Released:
DOI: 10.2210/pdb3dxu/pdb
PDB entry 3dxu coloured by chain, front view.
PDB entry 3dxu coloured by chain, side view.
PDB entry 3dxu coloured by chain, top view.
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
Assembly name:
PDBe Complex ID:
PDB-CPX-179408 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4D Chain: A
Molecule details ›
Chain: A
Length: 337 amino acids
Theoretical weight: 38.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6B0I6 (Residues: 11-341; Coverage: 63%)
Gene names: JHDM3D, JMJD2D, KDM4D
Sequence domains:
Structure domains: Cupin

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand FE2 1 x FE2
Ligand SO4 3 x SO4
Ligand OGA 1 x OGA
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P43212
Unit cell:
a: 71.543Å b: 71.543Å c: 150.194Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.221
Expression system: Escherichia coli

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