Structure of human urokinase plasminogen activator in complex with urokinase receptor and an anti-upar antibody at 1.9 a

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 47% strand (DSSP).

Ligands and binding sites

• ETX · 2-ethoxyethanol · ligand · 3 copies · chains L, U, H
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains U
• FUC · alpha-L-fucopyranose · sugar
• NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains U
• SO4 · Sulfate ion · ion · chains A, U
• EDO · 1,2-ethanediol · additive · 2 copies · chains L, H
• PGE · Triethylene glycol · additive · chains H, U
• PG4 · Tetraethylene glycol · additive · chains H, U

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• L–H · 1770 Ų buried · 20 hydrogen bonds · protein-protein
• A–U · 1125 Ų buried · 11 hydrogen bonds · protein-protein
• H–U · 433 Ų buried · 13 hydrogen bonds · protein-protein
• L–U · 261 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 23 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 2FD6 · Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and… · the same entry in another collection · chain A against A, TM-score 1.00
• Q03405 · AlphaFold monomer V2.0 prediction for urokinase plasminogen activator surface receptor… · a predicted model of the same protein · chain U against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P00749
• Every structure of UniProt Q52L64
• Every structure of UniProt Q4V9V8
• Every structure of UniProt Q03405
• Elsewhere: RCSB PDB 2FD6 · PDBe 2FD6 · UniProt P00749 · UniProt Q52L64 · UniProt Q4V9V8 · UniProt Q03405