› 5wbn

X-ray diffraction
1.64Å resolution

Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Released:
DOI: 10.2210/pdb5wbn/pdb
PDB entry 5wbn coloured by chain, front view.
PDB entry 5wbn coloured by chain, side view.
PDB entry 5wbn coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Harding RJ, Walker JR, Ferreira de Freitas R, Ravichandran M, Santhakumar V, Schapira M, Bountra C, Edwards AM, Arrowsmith CH

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193657 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 6 Chain: A
Molecule details ›
Chain: A
Length: 107 amino acids
Theoretical weight: 11.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBN7 (Residues: 1108-1213; Coverage: 9%)
Gene names: HDAC6, JM21, KIAA0901
Sequence domains: Zn-finger in ubiquitin-hydrolases and other protein
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

6 bound ligands:
Ligand ZN 3 x ZN
Ligand 9ZV 1 x 9ZV
Ligand UNX 8 x UNX
Ligand FMT 3 x FMT
Ligand CL 1 x CL
Ligand ACT 2 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 40.85Å b: 43.74Å c: 55.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.134 0.132 0.168
Expression system: Escherichia coli

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