Spike glycoprotein (S) is a 1173-residue protein from Human coronavirus 229E. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P15423.
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The mean pLDDT of this model is 68.7 (low 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 | 3% |
| 70 to 90 | Confident: backbone generally right | 55% |
| 50 to 70 | Low: treat with caution | 19% |
| Below 50 | Very low: often disordered regions | 22% |
What pLDDT means and how to read it
S1 region attaches the virion to the cell membrane by interacting with host ANPEP/aminopeptidase N, initiating the infection. Binding to the receptor probably induces conformational changes in the S glycoprotein unmasking the fusion peptide of S2 region and activating membranes fusion. S2 region belongs to the class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) regions assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the…
Homotrimer. During virus morphogenesis, found in a complex with M and HE proteins. Interacts with host ANPEP
Virion membrane, Host endoplasmic reticulum-Golgi intermediate compartment membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7EJM | X-ray | 1.71 Å | C=1110-1118 |
| 5YL9 | X-ray | 1.86 Å | A=784-872, B=1052-1104 |
| 5ZUV | X-ray | 2.21 Å | A/B/C=785-873 |
| 7YI6 | X-ray | 2.28 Å | A/C=835-841 |
| 5ZHY | X-ray | 2.44 Å | A/B/C/D/E/F=789-856, A/B/C/D/E/F=1053-1105 |
| 6U7H | EM | 3.1 Å | A/B/C=1-1113 |
| 7CYC | EM | 3.21 Å | A/B/C=1-1116 |
| 6ATK | X-ray | 3.5 Å | D/E/F=293-435 |
| 7CYD | EM | 3.55 Å | A/B/C=1-1116 |
| 8WDE | EM | 3.6 Å | A/B/C=15-1113 |
| 7VNG | X-ray | 3.8 Å | D=294-435 |
| 7VN9 | X-ray | 4.49 Å | C/E=294-435 |
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