› 5yc6

X-ray diffraction
1.18Å resolution

The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6

Released:
DOI: 10.2210/pdb5yc6/pdb
PDB entry 5yc6 coloured by chain, front view.
PDB entry 5yc6 coloured by chain, side view.
PDB entry 5yc6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases
Jiang LG, Zhang X, Zhou Y, Chen YY, Luo ZP, Li JY, Yuan C, Huang MD
RSC Adv 8 28189-28197 (2018)

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133249 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Urokinase-type plasminogen activator chain B Chain: U
Molecule details ›
Chain: U
Length: 246 amino acids
Theoretical weight: 27.72 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P00749 (Residues: 179-424; Coverage: 60%)
Gene name: PLAU
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

3 bound ligands:
Ligand PZH 1 x PZH
Ligand SO4 1 x SO4
Ligand PGE 2 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: R3
Unit cell:
a: 120.853Å b: 120.853Å c: 42.627Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.197 0.228
Expression system: Komagataella pastoris

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