› 3gv4

X-ray diffraction
1.72Å resolution

Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG

Released:
DOI: 10.2210/pdb3gv4/pdb
PDB entry 3gv4 coloured by chain, front view.
PDB entry 3gv4 coloured by chain, side view.
PDB entry 3gv4 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dong A, Ravichandran M, Loppnau P, Li Y, MacKenzie F, Kozieradzki I, Edwards AM, Arrowsmith CH, Weigelt J, Bountra C, Bochkarev A, Dhe-Paganon S, Min J, Ouyang H, Structural Genomics Consortium (SGC)

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
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163597 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 6 Chain: A
Molecule details ›
Chain: A
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 C-terminal peptide RLRGG Chain: H
Molecule details ›
Chain: H
Length: 5 amino acids
Theoretical weight: 560 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 31.657Å b: 36.093Å c: 88.998Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.174 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links