› 4mnv

X-ray diffraction
1.8Å resolution

Crystal structure of bicyclic peptide UK729 bound as an acyl-enzyme intermediate to urokinase-type plasminogen activator (uPA)

Released:
DOI: 10.2210/pdb4mnv/pdb
PDB entry 4mnv coloured by chain, front view.
PDB entry 4mnv coloured by chain, side view.
PDB entry 4mnv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Peptide ligands stabilized by small molecules.
Chen S, Bertoldo D, Angelini A, Pojer F, Heinis C
Angew Chem Int Ed Engl 53 1602-6 (2014)
PMID: 24453110

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133265 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 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
acyl-enzyme intermediate of bicyclic peptide UK729 Chain: B
Molecule details ›
Chain: B
Length: 10 amino acids
Theoretical weight: 1.16 KDa
Source organism: Homo sapiens
Expression system: Not provided
acyl-enzyme intermediate of bicyclic peptide UK729 Chain: C
Molecule details ›
Chain: C
Length: 4 amino acids
Theoretical weight: 317 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SO4 1 x SO4
Ligand ACT 2 x ACT
Ligand ZBR 1 x ZBR
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 52.31Å b: 54.06Å c: 79.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.216
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

12 review citations

Peptide therapeutics: targeting the undruggable space.
Tsomaia N. (2015)
11 more