MolNFT v1 · #13952 · protein
Heat-labile enterotoxin B-pentamer complexed with metanitrophenylgalactoside
1LT6: “Heat-labile enterotoxin B-pentamer complexed with metanitrophenylgalactoside”. X-ray diffraction, 1 ligand (GAA), 9 pockets (best druggability 0.71). MolNFT v1 #13952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1LT6
- Type
- protein
- Length
- 1,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat-labile enterotoxin
- UniProt
- P32890
- Ligands
- GAA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H, L, M, N, O, P | Heat-labile enterotoxin | protein | 103 | 24% helix, 37% strand | P32890 |
Ligands and binding sites
- GAA · 3-nitrophenyl alpha-D-galactopyranoside · ligand · 10 copies · chains D, E, F, G, H, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.71 | 0.76 | 43 | empty |
| 2 | 827 | 0.69 | 0.76 | 43 | empty |
| 3 | 56 | 0.43 | 0.83 | 19 | empty |
| 4 | 54 | 0.31 | 0.76 | 13 | GAA |
| 5 | 64 | 0.31 | 0.74 | 14 | GAA |
Interfaces
10 interfaces between chains.
- L–M · 1367 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1351 Ų buried · 27 hydrogen bonds · protein-protein
- M–N · 1347 Ų buried · 26 hydrogen bonds · protein-protein
- N–O · 1347 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 1325 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1LT6 · Heat-labile enterotoxin B-pentamer complexed with metanitrophenylgalactoside · the same entry in another collection · chain P against P, 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 P 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 1LT6 · PDBe 1LT6 · UniProt P32890
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