› 2xxz

X-ray diffraction
1.8Å resolution

Crystal structure of the human JMJD3 jumonji domain

Released:
DOI: 10.2210/pdb2xxz/pdb
PDB entry 2xxz coloured by chain, front view.
PDB entry 2xxz coloured by chain, side view.
PDB entry 2xxz coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Che KH, Yue WW, Krojer T, Muniz JRC, Ng SS, Tumber A, Daniel M, Burgess-Brown N, Savitsky P, Ugochukwu E, Filippakopoulos P, Arrowsmith C, Weigelt J, Edwards A, Bountra C, Oppermann U

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(27) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(27) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127275 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 6B Chains: A, B
Molecule details ›
Chains: A, B
Length: 332 amino acids
Theoretical weight: 37.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O15054 (Residues: 1176-1505; Coverage: 20%)
Gene names: JMJD3, KDM6B, KIAA0346
Sequence domains: JmjC domain, hydroxylase
Structure domains: Cupin

Ligands and Environments

4 bound ligands:
Ligand NI 3 x NI
Ligand NA 1 x NA
Ligand EDO 5 x EDO
Ligand 8XQ 2 x 8XQ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 56.757Å b: 71.431Å c: 159.698Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.216
Expression system: Escherichia coli BL21(DE3)

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