Crystal structure of piratoxin I (a myotoxic LYS49-PLA2) complexed with alpha-tocopherol

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 7% strand (DSSP).

Ligands and binding sites

• VIT · Vitamin E · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 5 copies · chains A, B
• PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains 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, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 522 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

• 3CYL · Crystal structure of Piratoxin I (a myotoxic Lys49-PLA2) complexed with alpha-tocopherol · the same entry in another collection · chain A against A, TM-score 1.00
• P82287 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog piratoxin-2 (P82287) · a predicted model of the same protein · chain A 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 P82287
• Elsewhere: RCSB PDB 3CYL · PDBe 3CYL · UniProt P82287