Cystal structure of myotoxin II from bothrops moojeni co-crystallized with varespladib (LY315920)

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 8% strand (DSSP).

Ligands and binding sites

• VRD · ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid · ligand · 2 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 682 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

• 6PWH · Cystal structure of Myotoxin II from Bothrops moojeni co-crystallized with Varespladib… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9I834 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog myotoxin II (Q9I834) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9I834
• Elsewhere: RCSB PDB 6PWH · PDBe 6PWH · UniProt Q9I834