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Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin, 1.9A crystal structure reveals the details
Analyse Novel binding site identified in a hybrid between cholera toxin and heat-labile… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EFX
- Type
- protein
- Length
- 961 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin subunit B, heat-labile enterotoxin B chain
- Ligands
- FUC, BGC, GAL, A2G
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 96 | 24% helix, 38% strand | — |
| E | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 96 | 24% helix, 38% strand | — |
| F | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 95 | 26% helix, 38% strand | — |
| G, I | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 95 | 23% helix, 38% strand | — |
| H | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 100 | 23% helix, 40% strand | — |
| J | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 93 | 25% helix, 41% strand | — |
| K | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 92 | 23% helix, 43% strand | — |
| L | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 97 | 25% helix, 37% strand | — |
| M | Cholera enterotoxin subunit B, heat-labile enterotoxin B chain | protein | 102 | 25% helix, 35% strand | — |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 20 copies · chains D, H, E, F, G, I, M, J, K, L
- BGC · beta-D-glucopyranose · sugar · 10 copies · chains D, E, F, G, H, I, J, K, L, M
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains D, E, F, G, H, I, J, K, L, M
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 10 copies · chains D, H, E, F, G, I, M, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.78 | 0.83 | 82 | empty |
| 2 | 637 | 0.71 | 0.79 | 38 | empty |
| 3 | 729 | 0.71 | 0.77 | 42 | empty |
| 4 | 183 | 0.56 | 0.80 | 23 | empty |
| 5 | 103 | 0.52 | 0.82 | 19 | empty |
Interfaces
20 interfaces between chains.
- F–G · 1214 Ų buried · 24 hydrogen bonds · protein-protein
- D–H · 1199 Ų buried · 22 hydrogen bonds · protein-protein
- J–K · 1167 Ų buried · 27 hydrogen bonds · protein-protein
- L–M · 1165 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1160 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3EFX · Novel binding site identified in a hybrid between cholera toxin and heat-labile… · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 3EFX · PDBe 3EFX
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