› 6ufn

X-ray diffraction
2.7Å resolution

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 7-[(3-aminopropyl)amino]heptan-2-one

Released:
DOI: 10.2210/pdb6ufn/pdb
PDB entry 6ufn coloured by chain, front view.
PDB entry 6ufn coloured by chain, side view.
PDB entry 6ufn coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation.
Herbst-Gervasoni CJ, Christianson DW
Biochemistry 58 4957-4969 (2019)
PMID: 31746596

Function and Biology Details

Reactions catalysed: 
N(8)-acetylspermidine + H(2)O = acetate + spermidine
N-acetylputrescine + H(2)O = acetate + putrescine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123343 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Polyamine deacetylase HDAC10 Chain: A
Molecule details ›
Chain: A
Length: 676 amino acids
Theoretical weight: 75.04 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: F1QCV2 (Residues: 2-675; Coverage: 100%)
Gene name: hdac10
Sequence domains: Histone deacetylase domain

Ligands and Environments

4 bound ligands:
Ligand Q6M 1 x Q6M
Ligand ZN 1 x ZN
Ligand PO4 4 x PO4
Ligand K 2 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-1
Spacegroup: P3121
Unit cell:
a: 80.547Å b: 80.547Å c: 246.201Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.192 0.19 0.228
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Structural determinants of affinity and selectivity in the binding of inhibitors to histone deacetylase 6.
Osko et al. (2020)
1 more

2 mentions without citation

Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation.
Herbst-Gervasoni et al. (2019)
1 more