Research workbench
Crystal structure of the B-subunit of the AB5 toxin from E. coli
Analyse Crystal structure of the B-subunit of the AB5 toxin from E. coli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DWA
- Type
- protein
- Length
- 588 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.084
- Source
- Escherichia coli
- Molecule
- Subtilase cytotoxin, subunit B
- UniProt
- Q3ZTX8
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.084 · 4 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subtilase cytotoxin, subunit B | protein | 118 | 19% helix, 41% strand | Q3ZTX8 |
| B, D | Subtilase cytotoxin, subunit B | protein | 117 | 20% helix, 40% strand | Q3ZTX8 |
| C | Subtilase cytotoxin, subunit B | protein | 120 | 19% helix, 40% strand | Q3ZTX8 |
| E | Subtilase cytotoxin, subunit B | protein | 116 | 20% helix, 41% strand | Q3ZTX8 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 5 copies · chains A, C, E, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.65 | 0.74 | 40 | 1PE |
| 2 | 68 | 0.30 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1064 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1059 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1053 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1048 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1028 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 9 disulfide (engineered, disulfide).
Compared structures
- 3DWA · Crystal structure of the B-subunit of the AB5 toxin from E. COLI · the same entry in another collection · chain A against A, TM-score 1.00
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 Q3ZTX8
- Elsewhere: RCSB PDB 3DWA · PDBe 3DWA · UniProt Q3ZTX8
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