Research workbench
Cholera toxin classical B-pentamer in complex with lewis-Y
Analyse Cholera toxin classical B-pentamer in complex with lewis-Y in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ELB
- Type
- protein
- Length
- 1,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin B subunit
- UniProt
- Q57193
- Ligands
- BCN, GAL, FUC, NDG, GLA, NAG, CA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cholera enterotoxin B subunit | protein | 103 | 24% helix, 39% strand | Q57193 |
Ligands and binding sites
- BCN · Bicine · ligand · 10 copies · chains A, G, H, E, B, F, C, J, D, I
- GAL · beta-D-galactopyranose · sugar · 20 copies · chains A, B, C, D, E, F, G, H, I, J
- FUC · alpha-L-fucopyranose · sugar · 20 copies · chains A, E, B, C, D, F, J, G, H, I
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- GLA · alpha-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H, I, J
- CA · Calcium ion · metal · 10 copies · chains A, H, E, B, G, C, F, D, J, I
- PEG · Di(hydroxyethyl)ether · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.80 | 0.86 | 62 | CA, BCN |
| 2 | 808 | 0.75 | 0.79 | 44 | empty |
| 3 | 320 | 0.75 | 0.86 | 36 | CA, BCN |
| 4 | 1007 | 0.74 | 0.77 | 43 | empty |
| 5 | 230 | 0.73 | 0.88 | 28 | CA, BCN |
Interfaces
20 interfaces between chains.
- G–H · 1306 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1293 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1292 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 1292 Ų buried · 24 hydrogen bonds · protein-protein
- F–J · 1287 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5ELB · Cholera toxin classical B-pentamer in complex with Lewis-y · the same entry in another collection · chain A against A, TM-score 1.00
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 Q57193
- Elsewhere: RCSB PDB 5ELB · PDBe 5ELB · UniProt Q57193
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