› 6thv

X-ray diffraction
1.1Å resolution

X-ray structure of the Danio rerio histone deacetylase 6 (HDAC6; catalytic domain 2) in complex with Tubastatin A

Released:
DOI: 10.2210/pdb6thv/pdb
PDB entry 6thv coloured by chain, front view.
PDB entry 6thv coloured by chain, side view.
PDB entry 6thv coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Structural and in Vivo Characterization of Tubastatin A, a Widely Used Histone Deacetylase 6 Inhibitor.
Shen S, Svoboda M, Zhang G, Cavasin MA, Motlova L, McKinsey TA, Eubanks JH, Bařinka C, Kozikowski AP
ACS Med Chem Lett 11 706-712 (2020)
PMID: 32435374

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 Chain: A
Molecule details ›
Chain: A
Length: 359 amino acids
Theoretical weight: 39.9 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

Ligands and Environments

8 bound ligands:
Ligand ZN 1 x ZN
Ligand K 3 x K
Ligand EDO 2 x EDO
Ligand PEG 2 x PEG
Ligand SCN 2 x SCN
Ligand NA 1 x NA
Ligand GOL 1 x GOL
Ligand N9W 1 x N9W
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P21212
Unit cell:
a: 84.278Å b: 93.713Å c: 51.574Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.16 0.169
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Tubulin Post-Translational Modifications: The Elusive Roles of Acetylation.
Carmona et al. (2023)
1 more

5 mentions without citation

Mercaptoacetamide: A promising zinc-binding group for the discovery of selective histone deacetylase 6 inhibitors.
Tavares et al. (2021)
4 more