MolNFT v1 · #13951 · protein
Heat-labile enterotoxin B-pentamer complexed with thiodigalactoside
1LT5: “Heat-labile enterotoxin B-pentamer complexed with thiodigalactoside”. X-ray diffraction, 2 ligands (YIO, GAL), 7 pockets (best druggability 0.72). MolNFT v1 #13951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1LT5
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat-labile enterotoxin
- UniProt
- P32890
- Ligands
- YIO, GAL
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H | Heat-labile enterotoxin | protein | 103 | 22% helix, 41% strand | P32890 |
Ligands and binding sites
- YIO · 1-thio-beta-D-galactopyranose · ligand · 5 copies · chains H, D, E, F, G
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains H, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.72 | 0.77 | 43 | empty |
| 2 | 58 | 0.35 | 0.78 | 18 | empty |
| 3 | 60 | 0.34 | 0.77 | 15 | empty |
| 4 | 60 | 0.31 | 0.76 | 15 | YIO |
| 5 | 54 | 0.29 | 0.75 | 14 | YIO |
Interfaces
5 interfaces between chains.
- D–E · 1401 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 1346 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 1311 Ų buried · 28 hydrogen bonds · protein-protein
- D–H · 1296 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1278 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1LT5 · Heat-labile enterotoxin B-pentamer complexed with thiodigalactoside · the same entry in another collection · chain H against H, TM-score 1.00
- P32890 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P32890) · a predicted model of the same protein · chain G 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 P32890
- Elsewhere: RCSB PDB 1LT5 · PDBe 1LT5 · UniProt P32890
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