X-ray diffraction
2.23Å resolution

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:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Lysine-specific histone demethylase 1B Chain: A
Molecule details ›
Chain: A
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:
Putative oxidoreductase GLYR1 Chain: B
Molecule details ›
Chain: B
Length: 124 amino acids
Theoretical weight: 13.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: Q49A26 (Residues: 152-268; Coverage: 21%)
Gene names: GLYR1, HIBDL, NDF, NP60
Histone H3.3 Chain: C
Molecule details ›
Chain: C
Length: 21 amino acids
Theoretical weight: 2.26 KDa
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: P84243 (Residues: 2-22; Coverage: 15%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P3221
Unit cell:
a: 101.083Å b: 101.083Å c: 177.372Å
α: 90° β: 90° γ: 120°
R R work R free
0.209 0.207 0.237
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli
  • Not provided