Pertussis toxin subunit 2 (ptxB) is a 226-residue protein from Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P04978.
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The mean pLDDT of this model is 90.5 (very high overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 84% |
| 70 to 90 | Confident: backbone generally right | 3% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 6% |
What pLDDT means and how to read it
PTX oligomer B binds to receptors on the eukaryotic cell surface and facilitates the translocation of the toxic subunit across the cell membrane
Pertussis toxin contains five different chains, S1-S5. They are organized into 2 functional subunits: A, composed of S1 (which is toxic) and B, containing S2, S3, S5, and two copies of S4 (B binds to the membrane receptors). Dimers of S2-S4 and S3-S4 are held together by S5
Secreted, Host cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6RO0 | X-ray | 2.13 Å | B/H=1-226 |
| 1BCP | X-ray | 2.7 Å | B/H=28-226 |
| 1PRT | X-ray | 2.9 Å | B/H=31-226 |
| 1PTO | X-ray | 3.5 Å | B=31-226, H=29-226 |
| 9MR7 | EM | 3.56 Å | B=28-226 |
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