3u4s

X-ray diffraction
2.15Å resolution

Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine

Released:

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-130866 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 4A Chains: A, B
Molecule details ›
Chains: A, B
Length: 381 amino acids
Theoretical weight: 44.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75164 (Residues: 1-359; Coverage: 34%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains:
Structure domains: Cupin
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 amino acids
Theoretical weight: 851 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 8-15; Coverage: 6%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, 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: DIAMOND BEAMLINE I04
Spacegroup: P21212
Unit cell:
a: 99.819Å b: 150.06Å c: 55.917Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.222
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided