› 4dm9

X-ray diffraction
2.35Å resolution

The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK

Released:
DOI: 10.2210/pdb4dm9/pdb
PDB entry 4dm9 coloured by chain, front view.
PDB entry 4dm9 coloured by chain, side view.
PDB entry 4dm9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK).
Davies CW, Chaney J, Korbel G, Ringe D, Petsko GA, Ploegh H, Das C
Bioorg Med Chem Lett 22 3900-4 (2012)
PMID: 22617491

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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140825 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase isozyme L1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 228 amino acids
Theoretical weight: 25.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09936 (Residues: 1-223; Coverage: 100%)
Gene name: UCHL1
Sequence domains: Ubiquitin carboxyl-terminal hydrolase, family 1
Structure domains: Peptidase C12, ubiquitin carboxyl-terminal hydrolase
Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 5 amino acids
Theoretical weight: 500 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand GME 2 x GME

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P4212
Unit cell:
a: 110.011Å b: 110.011Å c: 78.745Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.25
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Deubiquitylating enzymes and drug discovery: emerging opportunities.
Harrigan et al. (2018)
5 more

7 mentions without citation

Recent Advances in the Discovery of Deubiquitinating Enzyme Inhibitors.
Kemp M. (2016)
6 more