5efn

X-ray diffraction
1.8Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in complex with histone H4 Lys6 tripeptide substrate

Released:
Source organisms:
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-123748 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
UBP-type domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 364 amino acids
Theoretical weight: 40.22 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
histone H4 tripeptide Chains: E, F
Molecule details ›
Chains: E, F
Length: 3 amino acids
Theoretical weight: 420 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 54.997Å b: 83.908Å c: 86.903Å
α: 90° β: 98.12° γ: 90°
R-values:
R R work R free
0.164 0.162 0.194
Expression systems:
  • Escherichia coli
  • Not provided