Crystal structure of myotoxin II from bothrops moojeni complexed to suramin

Structure

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

Ligands and binding sites

• SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · 2 copies · chains B, A
• SO4 · Sulfate ion · ion · 7 copies · chains B, A
• 1PE · Pentaethylene glycol · additive · 2 copies · chains B, A
• 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.

• B–A · 567 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

• 4YV5 · Crystal Structure of Myotoxin II from Bothrops moojeni complexed to Suramin · 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 B against A, TM-score 0.96

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 4YV5 · PDBe 4YV5 · UniProt Q9I834