› 7ms6

X-ray diffraction
1.55Å resolution

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (2-fluoro-4-((4-phenylpiperidin-1-yl)sulfonyl)benzoyl)glycine

Released:
DOI: 10.2210/pdb7ms6/pdb
PDB entry 7ms6 coloured by chain, front view.
PDB entry 7ms6 coloured by chain, side view.
PDB entry 7ms6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Activity Relationship of USP5 Inhibitors.
Mann MK, Zepeda-Velázquez CA, González-Álvarez H, Dong A, Kiyota T, Aman AM, Loppnau P, Li Y, Wilson B, Arrowsmith CH, Al-Awar R, Harding RJ, Schapira M
J Med Chem 64 15017-15036 (2021)
PMID: 34648286

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
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-155377 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 5 Chain: A
Molecule details ›
Chain: A
Length: 121 amino acids
Theoretical weight: 13.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45974 (Residues: 171-290; Coverage: 14%)
Gene names: ISOT, USP5
Sequence domains: Zn-finger in ubiquitin-hydrolases and other protein

Ligands and Environments

4 bound ligands:
Ligand ZPV 1 x ZPV
Ligand SO4 1 x SO4
Ligand EDO 1 x EDO
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P43
Unit cell:
a: 53.575Å b: 53.575Å c: 54.097Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.149 0.148 0.164
Expression system: Escherichia coli

Quick links

Citations

2 review citations

PROTACs in the Management of Prostate Cancer.
Yedla et al. (2023)
1 more