X-ray diffraction
3.1Å resolution

Crystal structure of LSD2 with H3


Function and Biology Details

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + acceptor + H(2)O = a [histone H3]-N(6)-methyl-L-lysine(4) + formaldehyde + reduced acceptor

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific histone demethylase 1B Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 776 amino acids
Theoretical weight: 87.05 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
  • Canonical: Q8NB78 (Residues: 51-822; Coverage: 94%)
Gene names: AOF1, C6orf193, KDM1B, LSD2
Sequence domains:
Histone H3.3 Chains: E, F
Molecule details ›
Chains: E, F
Length: 26 amino acids
Theoretical weight: 2.79 KDa
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: P84243 (Residues: 2-27; Coverage: 19%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 101.843Å b: 108.926Å c: 120.825Å
α: 94.47° β: 112.34° γ: 117.95°
R R work R free
0.205 0.204 0.221
Expression systems:
  • Spodoptera frugiperda
  • Not provided