› 4jk5

X-ray diffraction
1.55Å resolution

Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide inhibitor (UK18-D-Ser)

Released:
DOI: 10.2210/pdb4jk5/pdb
PDB entry 4jk5 coloured by chain, front view.
PDB entry 4jk5 coloured by chain, side view.
PDB entry 4jk5 coloured by chain, top view.
Source organisms:
Primary publication:
Improving binding affinity and stability of peptide ligands by substituting glycines with D-amino acids.
Chen S, Gfeller D, Buth SA, Michielin O, Leiman PG, Heinis C
Chembiochem 14 1316-22 (2013)
PMID: 23828687

Function and Biology Details

Reaction catalysed: 
Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133263 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Urokinase-type plasminogen activator chain B Chain: A
Molecule details ›
Chain: A
Length: 245 amino acids
Theoretical weight: 27.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P00749 (Residues: 179-423; Coverage: 60%)
Gene name: PLAU
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
bicyclic peptide UK18-D-Ser, uPA inhibitor Chain: B
Molecule details ›
Chain: B
Length: 18 amino acids
Theoretical weight: 1.82 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SO4 4 x SO4
Ligand CL 2 x CL
Ligand P6G 1 x P6G
Ligand ZBR 1 x ZBR
1 modified residue:
Ligand DSN 1 x DSN

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: R3
Unit cell:
a: 121.239Å b: 121.239Å c: 42.631Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.146 0.142 0.213
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

6 review citations

Strategic approaches to optimizing peptide ADME properties.
Di L. (2015)
5 more