Spike glycoprotein (S) is a 1273-residue protein from Severe acute respiratory syndrome coronavirus 2. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P0DTC2.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 67.1 (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 | 20% |
| Below 50 | Very low: often disordered regions | 24% |
What pLDDT means and how to read it
Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. The major receptor is host ACE2 (PubMed:32142651, PubMed:32155444, PubMed:33607086). When S2/S2' has been cleaved, binding to the receptor triggers direct fusion at the cell membrane (PubMed:34561887). When S2/S2' has not been cleaved, binding to the receptor results in internalization of the virus by endocytosis using host TFRC and GRM2 and leading to fusion of the virion membrane with the host endosomal membrane (PubMed:32075877, PubMed:32221306, PubMed:34903715, PubMed:36779763). Alternatively, may use NRP1/NRP2 (PubMed:33082294, PubMed:33082293) and integrin as entry receptors…
Homotrimer; each monomer consists of a S1 and a S2 subunit (PubMed:32075877, PubMed:32155444, PubMed:32245784). The resulting peplomers protrude from the virus surface as spikes (PubMed:32979942). Interacts with ORF3a protein and ORF7a protein (By similarity) (PubMed:32075877, PubMed:32155444, PubMed:32245784, PubMed:32979942). There are an average of 26 +/-15 spike trimers at the surface of…
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 |
|---|---|---|---|
| 7Z8O | X-ray | 0.96 Å | A=333-527 |
| 7Y8J | X-ray | 1.03 Å | A=950-955 |
| 9FC2 | X-ray | 1.21 Å | A=332-534 |
| 7EK6 | X-ray | 1.24 Å | A=906-957, B=1175-1211 |
| 7EAM | X-ray | 1.4 Å | A/B=319-541 |
| 7M53 | X-ray | 1.4 Å | A=1146-1161 |
| 8CMC | X-ray | 1.42 Å | C=511-530 |
| 7M8U | X-ray | 1.45 Å | C=896-904 |
| 7ZR2 | X-ray | 1.45 Å | A=915-988, B=1164-1202 |
| 8D36 | X-ray | 1.45 Å | F=812-826 |
| 8ENS | X-ray | 1.45 Å | C=1267-1273 |
| 8ENW | X-ray | 1.45 Å | C/D=1267-1272 |
| 6M1V | X-ray | 1.5 Å | A=918-966, A=989-1032 |
| 7M8T | X-ray | 1.5 Å | C=370-378 |
| 7OAO | X-ray | 1.5 Å | EEE=330-532 |
| 8DTR | X-ray | 1.5 Å | G/J=1145-1159 |
| 7SD5 | X-ray | 1.53 Å | A=319-537 |
| 7OAQ | X-ray | 1.55 Å | EEE=330-532 |
| 7Z1D | X-ray | 1.55 Å | EEE=330-532 |
| 9IQP | X-ray | 1.55 Å | A=319-541 |
Showing 20 of 2199 experimental structures (best resolution first).
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.