PDBe 3phd

X-ray diffraction
3Å resolution

Crystal structure of human HDAC6 in complex with ubiquitin

Released:

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 6 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 107 amino acids
Theoretical weight: 12.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBN7 (Residues: 1109-1215; Coverage: 9%)
Gene names: HDAC6, JM21, KIAA0901
Sequence domains: Zn-finger in ubiquitin-hydrolases and other protein
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62987 (Residues: 1-76; Coverage: 59%)
Gene names: UBA52, UBCEP2
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P43212
Unit cell:
a: 133.748Å b: 133.748Å c: 118.768Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.235 0.265
Expression system: Escherichia coli