› 3c5k

X-ray diffraction
1.55Å resolution

Crystal structure of human HDAC6 zinc finger domain

Released:
DOI: 10.2210/pdb3c5k/pdb
PDB entry 3c5k coloured by chain, front view.
PDB entry 3c5k coloured by chain, side view.
PDB entry 3c5k coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dong A, Ravichandran M, Schuetz A, 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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193657 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 6 Chain: A
Molecule details ›
Chain: A
Length: 109 amino acids
Theoretical weight: 12.17 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)

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 40.5Å b: 45.109Å c: 55.759Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.173 0.227
Expression system: Escherichia coli

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