Crystal structure of isoform cbd of the basic phospholipase A2 subunit of crotoxin from crotalus durissus terrificus

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 3% strand (DSSP).

Ligands and binding sites

• NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F
• CL · Chloride ion · ion · 7 copies · chains A, B, F, C, D, E
• PG4 · Tetraethylene glycol · additive · 13 copies · chains A, F, B, C, D, E

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• A–C · 534 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 492 Ų buried · 6 hydrogen bonds · protein-protein
• D–E · 371 Ų buried · 9 hydrogen bonds · protein-protein
• B–F · 290 Ų buried · 6 hydrogen bonds · protein-protein
• C–E · 265 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 disulfide (disulfide).

Compared structures

• 6TMY · Crystal structure of isoform CBd of the basic phospholipase A2 subunit of crotoxin from… · the same entry in another collection · chain C against C, TM-score 1.00
• P62022 · AlphaFold monomer V2.0 prediction for phospholipase A2 crotoxin basic subunit cbc (P62022) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P62022
• Elsewhere: RCSB PDB 6TMY · PDBe 6TMY · UniProt P62022