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Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B
Analyse Novel structural insights for a pair of monoclonal antibodies recognizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SO7
- Type
- protein
- Length
- 1,919 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.59
- Source
- Clostridioides difficile; Homo sapiens
- Molecule
- Toxin B; Fab B1 HC; Fab B1 lc
- EC
- 3.4.22.-
- UniProt
- P18177
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · resolution 3.59 · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B (EC 3.4.22.-) | protein | 528 | 55% helix, 8% strand | P18177 |
| B | Toxin B (EC 3.4.22.-) | protein | 529 | 54% helix, 7% strand | P18177 |
| X, H | Fab B1 HC | protein | 213 | 1% helix, 49% strand | — |
| Y, L | Fab B1 lc | protein | 218 | 6% helix, 47% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.72 | 0.77 | 87 | empty |
| 2 | 716 | 0.70 | 0.77 | 77 | empty |
| 3 | 425 | 0.69 | 0.81 | 41 | empty |
| 4 | 459 | 0.69 | 0.80 | 35 | empty |
| 5 | 598 | 0.62 | 0.74 | 60 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1726 Ų buried · 11 hydrogen bonds · protein-protein
- X–Y · 1695 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1345 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 482 Ų buried · 8 hydrogen bonds · protein-protein
- B–X · 474 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7SO7 · Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P18177 · AlphaFold monomer V2.0 prediction for toxin B (P18177) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P18177
- Elsewhere: RCSB PDB 7SO7 · PDBe 7SO7 · UniProt P18177
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