Crystal structure of a papaya latex serine protease inhibitor (ppi) at 1.7A resolution

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 40% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
• CO · Cobalt (II) ion · metal · 2 copies · chains A
• SO4 · Sulfate ion · ion · 7 copies · chains A, B
• NH4 · Ammonium ion · ion · 3 copies · chains A, B
• GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 469 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 3S8K · Crystal structure of a papaya latex serine protease inhibitor (PPI) at 1.7A resolution · the same entry in another collection · chain A against A, TM-score 1.00
• P80691 · AlphaFold monomer V2.0 prediction for latex serine proteinase inhibitor (P80691) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 P80691
• Elsewhere: RCSB PDB 3S8K · PDBe 3S8K · UniProt P80691