H-2 class II histocompatibility antigen, A-D alpha chain (H2-Aa) is a 256-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P04228.
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The mean pLDDT of this model is 88.8 (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 | 73% |
| 70 to 90 | Confident: backbone generally right | 16% |
| 50 to 70 | Low: treat with caution | 9% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
Membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6BLQ | X-ray | 1.8 Å | A=24-208 |
| 7QHP | X-ray | 1.82 Å | A=24-218 |
| 6BLR | X-ray | 1.96 Å | A=26-208 |
| 6BLX | X-ray | 2.32 Å | A=26-208 |
| 2IAD | X-ray | 2.4 Å | A=24-209 |
| 5DMK | X-ray | 2.45 Å | A/C/E/G=26-198 |
| 1ES0 | X-ray | 2.6 Å | A=24-205 |
| 1IAO | X-ray | 2.6 Å | A=24-209 |
| 7Z50 | X-ray | 2.65 Å | A/C=24-218 |
| 3MBE | X-ray | 2.89 Å | A/E=24-205 |
| 7RDV | X-ray | 2.9 Å | A=28-205 |
| 3CUP | X-ray | 3.09 Å | A=24-205 |
| 1F3J | X-ray | 3.1 Å | A/D=27-208 |
| 6DFS | X-ray | 3.1 Å | C=26-208 |
| 6DFW | X-ray | 3.2 Å | A/C=26-208 |
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