2v5w

X-ray diffraction
2Å resolution

Function and Biology Details

Reaction catalysed:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone

Structure analysis Details

Assemblies composition:
hetero dimer
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-138112 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Histone deacetylase 8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 388 amino acids
Theoretical weight: 43.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BY41 (Residues: 1-377; Coverage: 100%)
Gene names: CDA07, HDAC8, HDACL1
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain
GLYCYL-GLYCYL-GLYCINE Chain: G
Molecule details ›
Chain: G
Length: 3 amino acids
Theoretical weight: 189 Da
Source organism: synthetic construct
Expression system: Not provided
Cellular tumor antigen p53 Chains: I, L
Molecule details ›
Chains: I, L
Length: 6 amino acids
Theoretical weight: 837 Da
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P04637 (Residues: 379-382; Coverage: 1%)
Gene names: P53, TP53

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 52.304Å b: 151.801Å c: 57.552Å
α: 90° β: 117.02° γ: 90°
R-values:
R R work R free
0.179 0.176 0.23
Expression systems:
  • Escherichia coli
  • Not provided