› 3rqd

X-ray diffraction
2.14Å resolution

Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8

Released:
DOI: 10.2210/pdb3rqd/pdb
PDB entry 3rqd coloured by chain, front view.
PDB entry 3rqd coloured by chain, side view.
PDB entry 3rqd coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases.
Cole KE, Dowling DP, Boone MA, Phillips AJ, Christianson DW
J Am Chem Soc 133 12474-7 (2011)
PMID: 21790156

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

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-163987 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 389 amino acids
Theoretical weight: 43.23 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
Largazole Chains: C, D
Molecule details ›
Chains: C, D
Length: 5 amino acids
Theoretical weight: 551 Da
Source organism: Symploca
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
2 modified residues:
Ligand BB9 2 x BB9
Ligand 03Y 2 x 03Y

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 54.059Å b: 88.302Å c: 93.66Å
α: 90° β: 101.62° γ: 90°
R-values:
R R work R free
0.204 0.202 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

31 review citations

Targeted cancer therapy: giving histone deacetylase inhibitors all they need to succeed.
Gryder et al. (2012)
30 more

21 mentions without citation

Erasers of histone acetylation: the histone deacetylase enzymes.
Seto et al. (2014)
20 more