Research workbench
Cholera holotoxin with an a-subunit Y30S mutation, crystal form 2
Analyse Cholera holotoxin with an a-subunit Y30S mutation, 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
- 1S5D
- Type
- protein
- Length
- 733 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
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholera enterotoxin, a chain (EC 2.4.2.36) | protein | 218 | 40% helix, 19% strand | P01555 |
| D, E, F, G, H | Cholera toxin B protein (ctb) | protein | 103 | 24% 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
- GOL · Glycerol · additive · 5 copies · chains A, F, G, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.74 | 0.82 | 52 | GOL |
| 2 | 371 | 0.71 | 0.83 | 57 | empty |
| 3 | 234 | 0.57 | 0.78 | 36 | GOL |
| 4 | 149 | 0.51 | 0.79 | 17 | empty |
| 5 | 119 | 0.44 | 0.77 | 18 | empty |
Interfaces
10 interfaces between chains.
- G–H · 1299 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1289 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1286 Ų buried · 25 hydrogen bonds · protein-protein
- D–H · 1272 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1229 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1S5D · Cholera holotoxin with an A-subunit Y30S mutation, 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 1S5D · PDBe 1S5D · UniProt P01555 · UniProt P01556
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