Research workbench
Cholera toxin B-pentamer complexed with GM1 pentasaccharide
Analyse Cholera toxin B-pentamer complexed with GM1 pentasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CHB
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera toxin
- UniProt
- P01556
- Ligands
- GAL, NGA, SIA, BGC
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H | Cholera toxin | protein | 103 | 22% helix, 38% strand | P01556 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains D, E, F, G, H
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 5 copies · chains D, E, F, G, H
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 5 copies · chains D, E, F, G, H
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.72 | 0.77 | 40 | empty |
| 2 | 58 | 0.31 | 0.75 | 11 | GAL |
Interfaces
5 interfaces between chains.
- D–E · 1368 Ų buried · 27 hydrogen bonds · protein-protein
- D–H · 1304 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1304 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1302 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1294 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2CHB · Cholera toxin B-pentamer complexed with GM1 pentasaccharide · 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 D 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 2CHB · PDBe 2CHB · UniProt P01556
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