› 5ix0

X-ray diffraction
1.72Å resolution

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187746 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 369 amino acids
Theoretical weight: 42.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92769 (Residues: 7-375; Coverage: 76%)
Gene name: HDAC2
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

8 bound ligands:
Ligand ZN 3 x ZN
Ligand CA 6 x CA
Ligand 6EZ 3 x 6EZ
Ligand PEG 5 x PEG
Ligand PG4 2 x PG4
Ligand PG5 3 x PG5
Ligand PGE 9 x PGE
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 92.195Å b: 97.473Å c: 139.254Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.18 0.2
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The Process and Strategy for Developing Selective Histone Deacetylase 3 Inhibitors.
Cao et al. (2018)
6 more

7 mentions without citation

Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases.
Frühauf et al. (2021)
6 more