Research workbench
Heat-labile enterotoxin B-pentamer with bound ligand BMSC001
Analyse Heat-labile enterotoxin B-pentamer with bound ligand BMSC001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FD7
- Type
- protein
- Length
- 1,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat-labile enterotoxin B chain
- UniProt
- P32890
- Ligands
- AI1
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H, L, M, N, O, P | Heat-labile enterotoxin B chain | protein | 103 | 25% helix, 37% strand | P32890 |
Ligands and binding sites
- AI1 · N-benzyl-3-(alpha-D-galactos-1-yl)-benzamide · 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
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.74 | 0.77 | 46 | empty |
| 2 | 1087 | 0.74 | 0.77 | 44 | empty |
| 3 | 92 | 0.44 | 0.79 | 24 | empty |
| 4 | 67 | 0.42 | 0.81 | 21 | empty |
| 5 | 73 | 0.42 | 0.80 | 18 | empty |
Interfaces
10 interfaces between chains.
- N–O · 1412 Ų buried · 30 hydrogen bonds · protein-protein
- L–M · 1407 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1399 Ų buried · 30 hydrogen bonds · protein-protein
- L–P · 1383 Ų buried · 34 hydrogen bonds · protein-protein
- D–H · 1375 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1FD7 · Heat-labile enterotoxin B-pentamer with bound ligand BMSC001 · 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 M 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 1FD7 · PDBe 1FD7 · UniProt P32890
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