› 5tht

X-ray diffraction
2.41Å resolution

Crystal Structure of G303A HDAC8 in complex with M344

Released:
DOI: 10.2210/pdb5tht/pdb
PDB entry 5tht coloured by chain, front view.
PDB entry 5tht coloured by chain, side view.
PDB entry 5tht coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8.
Porter NJ, Christianson NH, Decroos C, Christianson DW
Biochemistry 55 6718-6729 (2016)
PMID: 27933794

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, C, D
Molecule details ›
Chains: A, B, C, D
Length: 389 amino acids
Theoretical weight: 43.25 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 B3N 4 x B3N
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand EDO 27 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 97.7Å b: 83.81Å c: 99.78Å
α: 90° β: 91.72° γ: 90°
R-values:
R R work R free
0.182 0.18 0.212
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases.
Porter et al. (2019)
4 more

2 mentions without citation

Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8.
Porter et al. (2016)
1 more