› 5efj

X-ray diffraction
1.73Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with HC toxin

Released:
DOI: 10.2210/pdb5efj/pdb
PDB entry 5efj coloured by chain, front view.
PDB entry 5efj coloured by chain, side view.
PDB entry 5efj coloured by chain, top view.
Source organisms:
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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123746 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UBP-type domain-containing protein Chain: D
Molecule details ›
Chain: 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
HC toxin Chain: F
Molecule details ›
Chain: F
Length: 4 amino acids
Theoretical weight: 473 Da
Source organism: Bipolaris zeicola

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand GOL 1 x GOL
Ligand NO3 2 x NO3
Ligand EDO 3 x EDO
2 modified residues:
Ligand DPR 1 x DPR
Ligand DAL 1 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P21212
Unit cell:
a: 83.53Å b: 94.144Å c: 51.476Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.152 0.173
Expression system: Escherichia coli

Quick links

Citations

31 review citations

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

5 mentions without citation

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