› 5eef

X-ray diffraction
2.15Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 in complex with trichostatin A

Released:
DOI: 10.2210/pdb5eef/pdb
PDB entry 5eef coloured by chain, front view.
PDB entry 5eef coloured by chain, side view.
PDB entry 5eef 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

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, B
Molecule details ›
Chains: A, B
Length: 366 amino acids
Theoretical weight: 40.29 KDa
Source organism: Danio rerio
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F8W4B7 (Residues: 60-419; Coverage: 33%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

5 bound ligands:
Ligand ZN 2 x ZN
Ligand TSN 2 x TSN
Ligand NH4 4 x NH4
Ligand SO4 1 x SO4
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL14-1
Spacegroup: P21
Unit cell:
a: 52.876Å b: 123.717Å c: 55.186Å
α: 90° β: 113.85° γ: 90°
R-values:
R R work R free
0.213 0.211 0.255
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

33 review citations

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

9 mentions without citation

Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Hai et al. (2016)
8 more