HLA class II histocompatibility antigen, DQ alpha 1 chain (HLA-DQA1) is a 254-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P01909.
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The mean pLDDT of this model is 87.9 (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 | 67% |
| 70 to 90 | Confident: backbone generally right | 19% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to…
Heterodimer of an alpha and a beta subunit; also referred as MHC class II molecule. In the endoplasmic reticulum (ER) it forms a heterononamer; 3 MHC class II molecules bind to a CD74 homotrimer (also known as invariant chain or HLA class II histocompatibility antigen gamma chain). In the endosomal/lysosomal system; CD74 undergoes sequential degradation by various proteases; leaving a small…
Cell membrane, Endoplasmic reticulum membrane, Golgi apparatus, trans-Golgi network membrane, Endosome membrane, Lysosome membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1UVQ | X-ray | 1.8 Å | A=24-218 |
| 6U3M | X-ray | 1.9 Å | A/C=24-206 |
| 5KSA | X-ray | 2.0 Å | A=24-206 |
| 6MFG | X-ray | 2.0 Å | A/C=24-206 |
| 2NNA | X-ray | 2.1 Å | A=24-206 |
| 8W84 | X-ray | 2.1 Å | C=24-206 |
| 5KSV | X-ray | 2.19 Å | A=24-216 |
| 9EJG | X-ray | 2.2 Å | A=24-206 |
| 1S9V | X-ray | 2.22 Å | A/D=24-216 |
| 8W86 | X-ray | 2.24 Å | C/G=24-206 |
| 1JK8 | X-ray | 2.4 Å | A=27-206 |
| 6XP6 | X-ray | 2.4 Å | A/D=24-206 |
| 9EJH | X-ray | 2.45 Å | A=24-206 |
| 6MFF | X-ray | 2.6 Å | A=24-206 |
| 4OZF | X-ray | 2.7 Å | A=24-206 |
| 5KSU | X-ray | 2.73 Å | A/D=24-216 |
| 8W85 | X-ray | 2.77 Å | C/G=24-206 |
| 4OZH | X-ray | 2.8 Å | A/C=24-206 |
| 6U3N | X-ray | 2.8 Å | A=24-206 |
| 8W83 | X-ray | 2.82 Å | C/G/K/O=24-206 |
Showing 20 of 28 experimental structures (best resolution first).
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