› 5g0i

X-ray diffraction
1.99Å resolution

Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with Nexturastat A

Released:
DOI: 10.2210/pdb5g0i/pdb
PDB entry 5g0i coloured by chain, front view.
PDB entry 5g0i coloured by chain, side view.
PDB entry 5g0i coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Structural insights into HDAC6 tubulin deacetylation and its selective inhibition.
Miyake Y, Keusch JJ, Wang L, Saito M, Hess D, Wang X, Melancon BJ, Helquist P, Gut H, Matthias P
Nat Chem Biol 12 748-54 (2016)
PMID: 27454931

Function and Biology Details

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: 809 amino acids
Theoretical weight: 89.35 KDa
Source organism: Danio rerio
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: F8W4B7 (Residues: 25-831; Coverage: 75%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

5 bound ligands:
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand N4R 4 x N4R
Ligand CL 1 x CL
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2
Unit cell:
a: 162.56Å b: 52.83Å c: 186.42Å
α: 90° β: 108.92° γ: 90°
R-values:
R R work R free
0.175 0.174 0.2
Expression system: Spodoptera frugiperda

Quick links

Citations

24 review citations

The Search for Potent, Small-Molecule HDACIs in Cancer Treatment: A Decade After Vorinostat.
Zagni et al. (2017)
23 more

8 mentions without citation

A patent review of histone deacetylase 6 inhibitors in neurodegenerative diseases (2014-2019).
Shen et al. (2020)
7 more