› 2v5x

X-ray diffraction
2.25Å resolution

Crystal structure of HDAC8-inhibitor complex

Released:
DOI: 10.2210/pdb2v5x/pdb
PDB entry 2v5x coloured by chain, front view.
PDB entry 2v5x coloured by chain, side view.
PDB entry 2v5x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex.
Vannini A, Volpari C, Gallinari P, Jones P, Mattu M, Carfí A, De Francesco R, Steinkühler C, Di Marco S
EMBO Rep 8 879-84 (2007)
PMID: 17721440

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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189815 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 388 amino acids
Theoretical weight: 43.2 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

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand V5X 2 x V5X
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P212121
Unit cell:
a: 84.298Å b: 98.694Å c: 110.474Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.24
Expression system: Escherichia coli

Quick links

Citations

30 review citations

Chemical mechanisms of histone lysine and arginine modifications.
Smith et al. (2009)
29 more

23 mentions without citation

HDAC8 substrates: Histones and beyond.
Wolfson et al. (2013)
22 more