Gag-Pol polyprotein (gag-pol) is a 155-residue protein from Human immunodeficiency virus type 1 group M subtype B. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P04585.
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The mean pLDDT of this model is 83.8 (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 | 42% |
| 70 to 90 | Confident: backbone generally right | 46% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Mediates, with Gag polyprotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence (Psi). Gag-Pol polyprotein may regulate its own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, the polyprotein would promote translation, whereas at high concentration, the polyprotein would encapsidate genomic RNA and then shut off translation
Homotrimer; further assembles as hexamers of trimers (PubMed:19327811). Interacts with gp41 (via C-terminus) (By similarity). Interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group (PubMed:24500712). Interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during…
Host cell membrane, Host endosome, host multivesicular body, Virion membrane, Host nucleus, Host cytoplasm, Virion
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6DV4 | X-ray | 1.14 Å | A/B=489-587 |
| 6DIF | X-ray | 1.2 Å | A/B=489-587 |
| 6DV0 | X-ray | 1.2 Å | A/B=489-587 |
| 5DGU | X-ray | 1.22 Å | A/B=489-587 |
| 6E9A | X-ray | 1.22 Å | A/B=489-587 |
| 6DJ1 | X-ray | 1.26 Å | A/B=489-587 |
| 8F0F | X-ray | 1.29 Å | A/B=489-587 |
| 6E7J | X-ray | 1.3 Å | A/B=489-587 |
| 6DJ7 | X-ray | 1.31 Å | A/B=489-587 |
| 8ESX | X-ray | 1.35 Å | A/B=489-587 |
| 8ESY | X-ray | 1.35 Å | A/B=489-587 |
| 6DJ2 | X-ray | 1.36 Å | A/B=489-587 |
| 4U1J | X-ray | 1.38 Å | C=180-188 |
| 4U7V | X-ray | 1.38 Å | A/B=489-587 |
| 3QIO | X-ray | 1.4 Å | A=1014-1093, A=1105-1148 |
| 6DIL | X-ray | 1.48 Å | A/B=489-587 |
| 4Q1Y | X-ray | 1.5 Å | A/B=489-587 |
| 6J1W | X-ray | 1.5 Å | C=745-753 |
| 6PYL | X-ray | 1.52 Å | C=263-272 |
| 4U1H | X-ray | 1.59 Å | C=180-188 |
Showing 20 of 262 experimental structures (best resolution first).
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