› 7kut

X-ray diffraction
2.05Å resolution

Crystal Structure of Danio rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)

Released:
DOI: 10.2210/pdb7kut/pdb
PDB entry 7kut coloured by chain, front view.
PDB entry 7kut coloured by chain, side view.
PDB entry 7kut coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10.
Herbst-Gervasoni CJ, Christianson DW
Biochemistry 60 303-313 (2021)
PMID: 33449614

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: 678 amino acids
Theoretical weight: 75.19 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

7 bound ligands:
Ligand EDO 7 x EDO
Ligand X51 1 x X51
Ligand PEG 2 x PEG
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand PO4 4 x PO4
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3121
Unit cell:
a: 80.248Å b: 80.248Å c: 245.96Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.178 0.176 0.219
Expression system: Escherichia coli

Quick links

Citations

7 citation in other articles

First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement.
Herp et al. (2022)
6 more

2 mentions without citation

X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10.
Herbst-Gervasoni et al. (2021)
1 more