5efk

X-ray diffraction
1.82Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (Y745F mutant) in complex with alpha tubulin K40 tripeptide substrate

Released:
Source organism: Danio rerio
Primary publication:
Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-123747 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
UBP-type domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 364 amino acids
Theoretical weight: 40.27 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
alpha tubulin K40 tripeptide Chain: A
Molecule details ›
Chain: A
Length: 3 amino acids
Theoretical weight: 390 Da
Source organism: Danio rerio
Expression system: Escherichia coli

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P21212
Unit cell:
a: 83.277Å b: 94.667Å c: 51.622Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.157 0.183
Expression system: Escherichia coli