› 4fwe

X-ray diffraction
2.13Å resolution

Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A

Released:
DOI: 10.2210/pdb4fwe/pdb
PDB entry 4fwe coloured by chain, front view.
PDB entry 4fwe coloured by chain, side view.
PDB entry 4fwe 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

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-185462 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: C2221
Unit cell:
a: 93.691Å b: 96.273Å c: 182.797Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.203 0.246
Expression system: Escherichia coli

Quick links

Citations

19 review citations

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

6 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)
5 more