› 4fwf

X-ray diffraction
2.7Å resolution

Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic

Released:
DOI: 10.2210/pdb4fwf/pdb
PDB entry 4fwf coloured by chain, front view.
PDB entry 4fwf coloured by chain, side view.
PDB entry 4fwf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b.
Zhang Q, Qi S, Xu M, Yu L, Tao Y, Deng Z, Wu W, Li J, Chen Z, Wong J
Cell Res 23 225-41 (2013)
PMID: 23266887

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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159424 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific histone demethylase 2 Chain: A
Molecule details ›
Chain: A
Length: 796 amino acids
Theoretical weight: 89.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NB78 (Residues: 30-822; Coverage: 97%)
Gene names: AOF1, C6orf193, KDM1B, LSD2
Sequence domains:
Histone H3.1 Chain: E
Molecule details ›
Chain: E
Length: 20 amino acids
Theoretical weight: 2.19 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-21; Coverage: 15%)
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

2 bound ligands:
Ligand ZN 3 x ZN
Ligand FAD 1 x FAD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 110.444Å b: 98.544Å c: 101.358Å
α: 90° β: 96.08° γ: 90°
R-values:
R R work R free
0.207 0.206 0.237
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

19 review citations

Histone lysine demethylases as targets for anticancer therapy.
Højfeldt et al. (2013)
18 more

2 mentions without citation

Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions.
Lavi et al. (2013)
1 more