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Heat-labile enterotoxin B-pentamer complexed with M-carboxyphenyl- alpha-D-galactose
Analyse Heat-labile enterotoxin B-pentamer complexed with M-carboxyphenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJR
- 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
- BEZ, GLA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H | Heat-labile enterotoxin | protein | 103 | 21% helix, 37% strand | P32890 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 3 copies · chains F, G, H, D
- GLA · alpha-D-galactopyranose · sugar · 5 copies · chains D, E, F, G, H
- GOL · Glycerol · additive · 3 copies · chains D, G, H
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 | 1022 | 0.74 | 0.77 | 43 | empty |
| 2 | 52 | 0.39 | 0.81 | 17 | empty |
| 3 | 57 | 0.38 | 0.80 | 17 | empty |
| 4 | 76 | 0.38 | 0.78 | 23 | empty |
| 5 | 56 | 0.37 | 0.80 | 18 | empty |
Interfaces
5 interfaces between chains.
- D–H · 1403 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 1379 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1346 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1269 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1257 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1DJR · Heat-labile enterotoxin B-pentamer complexed with M-carboxyphenyl-alpha-D-galactose · 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 H 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 1DJR · PDBe 1DJR · UniProt P32890
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