› 5efh

X-ray diffraction
2.16Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with trifluoroketone transition state analogue

Released:
DOI: 10.2210/pdb5efh/pdb
PDB entry 5efh coloured by chain, front view.
PDB entry 5efh coloured by chain, side view.
PDB entry 5efh coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Hai Y, Christianson DW
Nat Chem Biol 12 741-7 (2016)
PMID: 27454933

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UBP-type domain-containing protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 364 amino acids
Theoretical weight: 40.29 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: F8W4B7 (Residues: 440-798; Coverage: 33%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

6 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand FKS 2 x FKS
Ligand BR 7 x BR
Ligand EDO 1 x EDO
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 74.659Å b: 92.414Å c: 96.158Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.242
Expression system: Escherichia coli

Quick links

Citations

32 review citations

Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics.
Ali et al. (2018)
31 more

5 mentions without citation

Structural determinants of affinity and selectivity in the binding of inhibitors to histone deacetylase 6.
Osko et al. (2020)
4 more