2pxj

X-ray diffraction
2Å resolution

The complex structure of JMJD2A and monomethylated H3K36 peptide

Released:
Source organism: Homo sapiens

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:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-130870 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 4A Chains: A, B
Molecule details ›
Chains: A, B
Length: 347 amino acids
Theoretical weight: 40.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O75164 (Residues: 2-348; Coverage: 33%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains:
Structure domains: Cupin
monomethylated Histone H3K36 peptide Chains: I, J
Molecule details ›
Chains: I, J
Length: 22 amino acids
Theoretical weight: 2.4 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21212
Unit cell:
a: 100.863Å b: 150.172Å c: 57.317Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.256 0.256 0.276
Expression systems:
  • Escherichia coli BL21
  • Not provided