Cholera toxin classical B-pentamer in complex with inhibitor PC262

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 37% strand (DSSP).

Ligands and binding sites

• 7BN · (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3, 4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid · ligand · 5 copies · chains A, B, C, D, E
• CA · Calcium ion · metal · 3 copies · chains C, D, E
• MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D, E
• PEG · Di(hydroxyethyl)ether · additive · chains E

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

Pockets

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

Interfaces

5 interfaces between chains.

• D–E · 1347 Ų buried · 27 hydrogen bonds · protein-protein
• C–D · 1302 Ų buried · 23 hydrogen bonds · protein-protein
• B–C · 1292 Ų buried · 21 hydrogen bonds · protein-protein
• A–E · 1286 Ų buried · 22 hydrogen bonds · protein-protein
• A–B · 1259 Ų buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified, 5 disulfide (oxidation, disulfide).

Compared structures

• 5LZH · Cholera toxin classical B-pentamer in complex with inhibitor PC262 · the same entry in another collection · chain A 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 Q57193
• Elsewhere: RCSB PDB 5LZH · PDBe 5LZH · UniProt Q57193