PDBe 4tn7

X-ray diffraction
2.2Å resolution

Crystal structure of mouse KDM2A-H3K36ME-NO complex

Released:

Function and Biology Details

Reaction catalysed:
(1a) [protein]-N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = [protein]-N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Lysine-specific demethylase 2A Chains: A, C
Molecule details ›
Chains: A, C
Length: 329 amino acids
Theoretical weight: 39.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P59997 (Residues: 36-364; Coverage: 28%)
Gene names: Fbxl11, Jhdm1a, Kdm2a, Kiaa1004
Structure domains: Cupin
Lysine-specific demethylase 2A Chains: B, D
Molecule details ›
Chains: B, D
Length: 68 amino acids
Theoretical weight: 7.53 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P59997 (Residues: 450-517; Coverage: 6%)
Gene names: Fbxl11, Jhdm1a, Kdm2a, Kiaa1004
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Histone H3.1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 15 amino acids
Theoretical weight: 1.65 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 30-44; Coverage: 11%)
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

3 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 55.063Å b: 157.928Å c: 48.706Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.229 0.279
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided