Cholera toxin B-pentamer complexed with bivalent nitrophenol-galactoside ligand BV1

Structure

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

Ligands and binding sites

• BV1 · [3-(4-{3-[3-nitro-5-(galactopyranosyloxy)-benzoylamino]-propyl}-piperazin-1-yl)-propylamino] -2-(3-{4-[3-(3-nitro-5-[galactopyranosyloxy]-benzoylamino)-propyl]-piperazin-1-yl} -propyl-amino)-3,4-dioxo-cyclobutene · ligand · 5 copies · chains D, E, F, G, H

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

Pockets

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

Interfaces

5 interfaces between chains.

• G–H · 1339 Ų buried · 26 hydrogen bonds · protein-protein
• E–F · 1312 Ų buried · 20 hydrogen bonds · protein-protein
• D–E · 1295 Ų buried · 23 hydrogen bonds · protein-protein
• F–G · 1288 Ų buried · 25 hydrogen bonds · protein-protein
• D–H · 1272 Ų buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

• 1RCV · Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV1 · the same entry in another collection · chain F against F, TM-score 1.00
• P01556 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit B (P01556) · a predicted model of the same protein · chain F 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 1RCV · PDBe 1RCV · UniProt P01556