› 5ok6

X-ray diffraction
1.3Å resolution

Ubiquitin specific protease 11 USP11 - peptide F complex

Released:
DOI: 10.2210/pdb5ok6/pdb
PDB entry 5ok6 coloured by chain, front view.
PDB entry 5ok6 coloured by chain, side view.
PDB entry 5ok6 coloured by chain, top view.
Source organisms:
Primary publication:
Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11.
Spiliotopoulos A, Blokpoel Ferreras L, Densham RM, Caulton SG, Maddison BC, Morris JR, Dixon JE, Gough KC, Dreveny I
J Biol Chem 294 424-436 (2019)
PMID: 30373771

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156411 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 11 Chains: A, B
Molecule details ›
Chains: A, B
Length: 230 amino acids
Theoretical weight: 26.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51784 (Residues: 67-288; Coverage: 23%)
Gene names: UHX1, USP11
Sequence domains:
ALA-GLU-GLY-GLU-PHE-TYR-LYS-LEU-LYS-ILE-ARG-THR-PRO-AAR Chains: C, D
Molecule details ›
Chains: C, D
Length: 14 amino acids
Theoretical weight: 1.71 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand EDO 2 x EDO
1 modified residue:
Ligand AAR 2 x AAR

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 65.77Å b: 45.51Å c: 100.61Å
α: 90° β: 102.68° γ: 90°
R-values:
R R work R free
0.158 0.157 0.178
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Cancer Vaccines, Adjuvants, and Delivery Systems.
Paston et al. (2021)
5 more

1 mention without citation

Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11.
Spiliotopoulos et al. (2019)