Spike glycoprotein (S) is a 1352-residue protein from Bat coronavirus HKU5. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: A3EXD0.
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The mean pLDDT of this model is 66.2 (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 | 7% |
| 70 to 90 | Confident: backbone generally right | 49% |
| 50 to 70 | Low: treat with caution | 16% |
| Below 50 | Very low: often disordered regions | 28% |
What pLDDT means and how to read it
Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection
Homotrimer; each monomer consists of a S1 and a S2 subunit. The resulting peplomers protrude from the virus surface as spikes
Virion membrane, Host endoplasmic reticulum-Golgi intermediate compartment membrane, Host cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9EA0 | EM | 2.0 Å | A/B/C=22-1295 |
| 9EH8 | EM | 2.0 Å | A/B/C=22-1295 |
| 5XGR | X-ray | 2.1 Å | A/B/C/D/E/F/G/H=389-586 |
| 9KR8 | EM | 2.39 Å | A/B/C=1-1352 |
| 9DAK | EM | 2.4 Å | B=364-585 |
| 9E0I | EM | 2.4 Å | B=388-586 |
| 9N7D | EM | 2.5 Å | B=390-589 |
| 9N7E | EM | 2.5 Å | B=387-589 |
| 9KR9 | EM | 2.8 Å | A/B/C=1-1352 |
| 9KRA | EM | 2.8 Å | A=388-586 |
| 9JJ6 | EM | 2.94 Å | B=367-587 |
| 9D32 | EM | 3.1 Å | B=388-586 |
| 9KRB | EM | 3.22 Å | A=388-586 |
| 8ZUF | EM | 3.31 Å | B=390-512 |
| 9MV0 | EM | 4.2 Å | B/D=1-1352 |
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