Research workbench
Cholera holotoxin, crystal form 2
Analyse Cholera holotoxin, crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S5F
- Type
- protein
- Length
- 738 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin, a chain; Cholera toxin B protein (ctb)
- EC
- 2.4.2.36
- UniProt
- P01555, P01556
- Ligands
- GAL, NA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholera enterotoxin, a chain (EC 2.4.2.36) | protein | 224 | 37% helix, 21% strand | P01555 |
| D, E, F, H | Cholera toxin B protein (ctb) | protein | 103 | 25% helix, 35% strand | P01556 |
| G | Cholera toxin B protein (ctb) | protein | 102 | 21% helix, 36% strand | P01556 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains D, E, F, G, H
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.76 | 0.84 | 56 | empty |
| 2 | 287 | 0.70 | 0.84 | 35 | empty |
| 3 | 94 | 0.58 | 0.87 | 17 | empty |
| 4 | 146 | 0.52 | 0.80 | 26 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1347 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1267 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1266 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1211 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1200 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1S5F · Cholera holotoxin, Crystal form 2 · the same entry in another collection · chain H against H, TM-score 1.00
- P01555 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit a (P01555) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P01556 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit B (P01556) · a predicted model of the same protein · chain H 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 P01555
- Every structure of UniProt P01556
- Elsewhere: RCSB PDB 1S5F · PDBe 1S5F · UniProt P01555 · UniProt P01556
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