Protein Nef (nef) is a 123-residue protein from Human immunodeficiency virus type 1 group M subtype B. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P04601.
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The mean pLDDT of this model is 67.8 (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 | 0% |
| 70 to 90 | Confident: backbone generally right | 50% |
| 50 to 70 | Low: treat with caution | 40% |
| Below 50 | Very low: often disordered regions | 10% |
What pLDDT means and how to read it
Factor of infectivity and pathogenicity, required for optimal virus replication. Alters numerous pathways of T-lymphocyte function and down-regulates immunity surface molecules in order to evade host defense and increase viral infectivity. Alters the functionality of other immunity cells, like dendritic cells, monocytes/macrophages and NK cells
Monomer; cytosolic form. Homodimer; membrane bound form. Interacts with Nef associated p21-activated kinase (PAK2); this interaction activates PAK2. Associates with the Nef-MHC-I-AP1 complex; this complex is required for MHC-I internalization. Interacts (via C-terminus) with host PI3-kinase. Interacts with host PACS1; this interaction seems to be weak. Interacts with host PACS2. Interacts with…
Host cell membrane, Virion, Secreted, Host Golgi apparatus membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7YG3 | X-ray | 1.5 Å | B=106-114 |
| 7K81 | X-ray | 2.0 Å | C=134-141 |
| 5HGD | X-ray | 2.07 Å | C/F=134-143 |
| 5HGA | X-ray | 2.2 Å | C/F=134-141 |
| 4WU7 | X-ray | 2.3 Å | C/F=134-141 |
| 3RL2 | X-ray | 2.39 Å | C=73-82 |
| 5HGH | X-ray | 2.39 Å | C=134-143 |
| 4WU5 | X-ray | 2.4 Å | C/F=134-141 |
| 5HGB | X-ray | 2.4 Å | C/F/I/L=134-141 |
| 7K80 | X-ray | 2.4 Å | C/F=134-141 |
| 9BL9 | X-ray | 2.6 Å | C=134-141 |
| 4NEE | X-ray | 2.88 Å | C/E/H/K=63-203 |
| 9BLA | X-ray | 3.0 Å | C=134-141 |
| 8GVB | X-ray | 3.2 Å | P=134-141 |
| 8GVI | X-ray | 3.3 Å | P=134-141 |
| 8GVG | X-ray | 3.37 Å | P=134-141 |
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