MolNFT v1 · #117878 · protein
Cholera toxin el tor B-pentamer in complex with a-pentasaccharide
5ELF · Cholera enterotoxin subunit B: “Cholera toxin el tor B-pentamer in complex with a-pentasaccharide”. X-ray diffraction, 7 ligands (BCN, FUC, GAL), 10 pockets (best druggability 0.83). MolNFT v1 #117878 on GenesisL1: 3D structure…
- PDB
- 5ELF
- Type
- protein
- Length
- 1,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin subunit B
- UniProt
- P01556
- Ligands
- BCN, FUC, GAL, A2G, GLC, BGC, CA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cholera enterotoxin subunit B | protein | 103 | 22% helix, 37% strand | P01556 |
Ligands and binding sites
- BCN · Bicine · ligand · 10 copies · chains A, E, F, J, B, I, C, H, D, G
- FUC · alpha-L-fucopyranose · sugar · 16 copies · chains A, E, D, C, F, J, G, I, H, B
- GAL · beta-D-galactopyranose · sugar · 7 copies · chains A, D, E, F, G, I, J
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 7 copies · chains A, D, E, F, G, I, J
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, E, I, J, D, G
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains D, F, G
- CA · Calcium ion · metal · 10 copies · chains A, E, F, J, B, I, C, H, D, G
- PG4 · Tetraethylene glycol · additive · chains F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.83 | 0.85 | 98 | CA, BCN |
| 2 | 833 | 0.75 | 0.79 | 41 | empty |
| 3 | 1012 | 0.75 | 0.77 | 40 | empty |
| 4 | 420 | 0.74 | 0.84 | 60 | CA, BCN |
| 5 | 52 | 0.39 | 0.81 | 15 | empty |
Interfaces
23 interfaces between chains.
- C–D · 1344 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1329 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1322 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 1320 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1306 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5ELF · Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide · the same entry in another collection · chain J against J, TM-score 1.00
- P01556 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit B (P01556) · a predicted model of the same protein · chain B 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 5ELF · PDBe 5ELF · UniProt P01556
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