4o64

X-ray diffraction
2.13Å resolution

Zinc fingers of KDM2B

Released:

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 2B Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 118 amino acids
Theoretical weight: 13.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NHM5 (Residues: 607-723; Coverage: 9%)
Gene names: CXXC2, FBL10, FBXL10, JHDM1B, KDM2B, NDY1, PCCX2
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P31
Unit cell:
a: 107.322Å b: 107.322Å c: 34.13Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.19 0.22
Expression system: Escherichia coli BL21(DE3)