› 3ezp

X-ray diffraction
2.65Å resolution

Crystal Structure Analysis of human HDAC8 D101N variant

Released:
DOI: 10.2210/pdb3ezp/pdb
PDB entry 3ezp coloured by chain, front view.
PDB entry 3ezp coloured by chain, side view.
PDB entry 3ezp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.
Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW
Biochemistry 47 13554-63 (2008)
PMID: 19053282

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: 43.17 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

4 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand B3N 2 x B3N
Ligand BME 2 x BME
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 55.31Å b: 85.874Å c: 94.642Å
α: 90° β: 93.6° γ: 90°
R-values:
R R work R free
0.225 0.225 0.262
Expression system: Escherichia coli

Quick links

Citations

20 review citations

HDACs and HDAC Inhibitors in Cancer Development and Therapy.
Li et al. (2016)
19 more

7 mentions without citation

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