Crystal structure of the glycoprotein VI loop truncation mutant pavs- papykn

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 53% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
• CL · Chloride ion · ion · 14 copies · chains A, B, C, D
• PO4 · Phosphate ion · ion · 2 copies · chains A, B
• PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–C · 873 Ų buried · 12 hydrogen bonds · protein-protein
• B–D · 871 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 5OU7 · Crystal structure of the Glycoprotein VI loop truncation mutant PAVS-PAPYKN · the same entry in another collection · chain A against A, TM-score 1.00
• Q9HCN6 · AlphaFold monomer V2.0 prediction for platelet glycoprotein VI (Q9HCN6) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 Q9HCN6
• Elsewhere: RCSB PDB 5OU7 · PDBe 5OU7 · UniProt Q9HCN6