› 5ef8

X-ray diffraction
2.6Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with panobinostat

Released:
DOI: 10.2210/pdb5ef8/pdb
PDB entry 5ef8 coloured by chain, front view.
PDB entry 5ef8 coloured by chain, side view.
PDB entry 5ef8 coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Hai Y, Christianson DW
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
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UBP-type domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 364 amino acids
Theoretical weight: 40.29 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

Ligands and Environments

5 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand LBH 2 x LBH
Ligand GOL 3 x GOL
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P21212
Unit cell:
a: 65.168Å b: 140.396Å c: 91.856Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.189 0.234
Expression system: Escherichia coli

Quick links

Citations

31 review citations

Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics.
Ali et al. (2018)
30 more

12 mentions without citation

Impact of the Protein Data Bank on antineoplastic approvals.
Westbrook et al. (2020)
11 more