Cholera toxin B-pentamer complexed with bivalent nitrophenol-galactoside ligand BV3

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 36% strand (DSSP).

Ligands and binding sites

• BV3 · 1,3-bis-([[3-(4-{3-[3-nitro-5-(galactopyranosyloxy)-benzoylamino]-propyl}-piperazin-1-yl)-propylamino-3,4-dioxo-cyclobu tenyl]-amino-ethyl]-amino-carbonyloxy)-2-amino-propane · ligand · 5 copies · chains D, E, F, G, H
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D, H
• PGE · Triethylene glycol · additive · chains D, H

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

Pockets

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

Interfaces

5 interfaces between chains.

• D–H · 1331 Ų buried · 26 hydrogen bonds · protein-protein
• E–F · 1309 Ų buried · 25 hydrogen bonds · protein-protein
• G–H · 1308 Ų buried · 26 hydrogen bonds · protein-protein
• F–G · 1306 Ų buried · 23 hydrogen bonds · protein-protein
• D–E · 1277 Ų buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

• 1RDP · Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3 · the same entry in another collection · chain H against H, TM-score 1.00
• P01556 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit B (P01556) · a predicted model of the same protein · chain G against A, TM-score 0.99

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 P01556
• Elsewhere: RCSB PDB 1RDP · PDBe 1RDP · UniProt P01556