› 7d4a

X-ray diffraction
2.2Å resolution

The Crystal Structure of human JMJD2A Tudor domain from Biortus

Released:
DOI: 10.2210/pdb7d4a/pdb
PDB entry 7d4a coloured by chain, front view.
PDB entry 7d4a coloured by chain, side view.
PDB entry 7d4a coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Wang F, Lv Z, Cheng W, Lin D, Ju C, Bao X, Zhu B

Function and Biology Details

Reactions 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)
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130863 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4A Chain: A
Molecule details ›
Chain: A
Length: 131 amino acids
Theoretical weight: 15.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75164 (Residues: 898-1011; Coverage: 11%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains: Jumonji domain-containing protein 2A Tudor domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: I4132
Unit cell:
a: 135.11Å b: 135.11Å c: 135.11Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.23 0.272
Expression system: Escherichia coli

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