› 5xg4

X-ray diffraction
3Å resolution

Crystal structure of uPA in complex with quercetin

Released:
DOI: 10.2210/pdb5xg4/pdb
PDB entry 5xg4 coloured by chain, front view.
PDB entry 5xg4 coloured by chain, side view.
PDB entry 5xg4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A structural mechanism of flavonoids in inhibiting serine proteases.
Xue G, Gong L, Yuan C, Xu M, Wang X, Jiang L, Huang M
Food Funct 8 2437-2443 (2017)
PMID: 28644504

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

2 bound ligands:
Ligand QUE 1 x QUE
Ligand PG6 1 x PG6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NFPSS BEAMLINE BL19U1
Spacegroup: R3
Unit cell:
a: 119.969Å b: 119.969Å c: 41.78Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.17 0.258
Expression system: Komagataella pastoris

Quick links

Citations

7 review citations

Tackling the cytokine storm in COVID-19, challenges and hopes.
Abdin et al. (2020)
6 more

1 mention without citation

Comparative analysis of the reactivity of anthocyanidins, leucoanthocyanidins, and flavonols using a quantum chemistry approach.
de Souza Farias et al. (2023)