Research workbench
Clostridium perfringens enterotoxin, D48A mutation and N- terminal 37 residues deleted
Analyse Clostridium perfringens enterotoxin, D48A mutation and N- terminal 37 residues… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZIW
- Type
- protein
- Length
- 1,716 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat-labile enterotoxin B chain
- UniProt
- P01558
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Heat-labile enterotoxin B chain | protein | 286 | 11% helix, 54% strand | P01558 |
Ligands and binding sites
- P6G · Hexaethylene glycol · additive · 14 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.85 | 0.86 | 156 | P6G |
| 2 | 1097 | 0.85 | 0.86 | 163 | P6G |
| 3 | 999 | 0.74 | 0.77 | 100 | empty |
| 4 | 66 | 0.55 | 0.88 | 26 | empty |
| 5 | 63 | 0.52 | 0.87 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–D · 960 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 960 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 949 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 928 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 926 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3ZIW · Clostridium perfringens enterotoxin, D48A mutation and N-terminal 37 residues deleted · the same entry in another collection · chain F against F, TM-score 1.00
- P01558 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P01558) · a predicted model of the same protein · chain B 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 P01558
- Elsewhere: RCSB PDB 3ZIW · PDBe 3ZIW · UniProt P01558
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