MHC class II antigen (HLA-DQB1) is a 261-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Jun 2022. UniProt accession: A0A0U5Q247.
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The mean pLDDT of this model is 85.1 (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 | 66% |
| 70 to 90 | Confident: backbone generally right | 12% |
| 50 to 70 | Low: treat with caution | 17% |
| Below 50 | Very low: often disordered regions | 6% |
What pLDDT means and how to read it
Endosome membrane, Lysosome membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5KSA | X-ray | 2.0 Å | B=33-224 |
| 5KS9 | X-ray | 2.55 Å | B/D=33-224 |
| 5KSB | X-ray | 2.9 Å | B/D=33-224 |
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.