Spike glycoprotein (S) is a 1356-residue protein from Human coronavirus HKU1. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: Q5MQD0.
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The mean pLDDT of this model is 68.9 (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 | 54% |
| 50 to 70 | Low: treat with caution | 17% |
| Below 50 | Very low: often disordered regions | 22% |
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 |
|---|---|---|---|
| 9JCY | X-ray | 1.8 Å | A=323-609 |
| 5KWB | X-ray | 1.91 Å | A=307-677 |
| 9BT2 | EM | 1.93 Å | A=14-1298 |
| 9BSW | EM | 2.06 Å | A/B/C=14-1298 |
| 7EJN | X-ray | 2.11 Å | C=1295-1303 |
| 9BT9 | EM | 2.11 Å | A=14-1298 |
| 9BT1 | EM | 2.22 Å | A/B/C=14-1298 |
| 9BT0 | EM | 2.23 Å | A/B/C=14-1298 |
| 5GNB | X-ray | 2.3 Å | A=307-677 |
| 9BTB | EM | 2.33 Å | A=14-1298 |
| 9BSX | EM | 2.37 Å | A/B/C=14-1298 |
| 9BTA | EM | 2.39 Å | A=14-1298 |
| 9IZN | X-ray | 2.4 Å | A=307-677 |
| 9BTC | EM | 2.41 Å | A=14-1223 |
| 9BTD | EM | 2.43 Å | A/B/C=14-1298 |
| 9BSZ | EM | 2.49 Å | A/B/C=14-1298 |
| 9BSY | EM | 2.58 Å | A/B/C=14-1298 |
| 9JCX | X-ray | 2.75 Å | B=323-609 |
| 8DGW | X-ray | 2.81 Å | G/I/J/K=1226-1250 |
| 8VGT | EM | 2.9 Å | A=320-614 |
Showing 20 of 31 experimental structures (best resolution first).
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