Research workbench
Cholera holotoxin with an a-subunit Y30S mutation, crystal form 1
Analyse Cholera holotoxin with an a-subunit Y30S mutation, crystal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S5C
- Type
- protein
- Length
- 731 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin, a chain; Cholera enterotoxin B-subunit
- EC
- 2.4.2.36
- UniProt
- P01555, P01556
- Ligands
- NA
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholera enterotoxin, a chain (EC 2.4.2.36) | protein | 216 | 39% helix, 20% strand | P01555 |
| D, E, F, G, H | Cholera enterotoxin B-subunit | protein | 103 | 24% helix, 36% strand | P01556 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.72 | 0.78 | 64 | empty |
| 2 | 390 | 0.68 | 0.81 | 49 | empty |
| 3 | 258 | 0.57 | 0.78 | 34 | empty |
Interfaces
10 interfaces between chains.
- D–H · 1304 Ų buried · 31 hydrogen bonds · protein-protein
- F–G · 1271 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1269 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1235 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1228 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1S5C · Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 1 · the same entry in another collection · chain D against D, 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
- 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 0.98
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 1S5C · PDBe 1S5C · UniProt P01555 · UniProt P01556
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