Islet-activating protein S2 (ptxB) is a 226-residue protein from Bordetella pertussis. This is its AlphaFold structure prediction, created 1 Jun 2022. UniProt accession: A0A0E8DFW5.
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The mean pLDDT of this model is 88.4 (confident 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 | 79% |
| 70 to 90 | Confident: backbone generally right | 8% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 13% |
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
Host cell membrane, Secreted
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9E3H | EM | 2.9 Å | B=1-226 |
| 9E3K | EM | 3.2 Å | B=1-226 |
| 9E3L | EM | 3.4 Å | B=1-226 |
| 9E3J | EM | 3.6 Å | B=1-226 |
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