› 5fcw

X-ray diffraction
1.98Å resolution

HDAC8 Complexed with a Hydroxamic Acid

Released:
DOI: 10.2210/pdb5fcw/pdb
PDB entry 5fcw coloured by chain, front view.
PDB entry 5fcw coloured by chain, side view.
PDB entry 5fcw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of 'linkerless' hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket.
Tabackman AA, Frankson R, Marsan ES, Perry K, Cole KE
J Struct Biol 195 373-378 (2016)
PMID: 27374062

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: 383 amino acids
Theoretical weight: 42.63 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

5 bound ligands:
Ligand 5YA 4 x 5YA
Ligand ZN 2 x ZN
Ligand K 2 x K
Ligand P6G 1 x P6G
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 53.443Å b: 84.548Å c: 94.307Å
α: 90° β: 100.08° γ: 90°
R-values:
R R work R free
0.174 0.172 0.216
Expression system: Escherichia coli

Quick links

Citations

4 review citations

A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library.
Wang et al. (2019)
3 more

10 mentions without citation

A Therapeutic Perspective of HDAC8 in Different Diseases: An Overview of Selective Inhibitors.
Fontana et al. (2022)
9 more