DNA primase large subunit (PRI2) is a 528-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P20457.
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The mean pLDDT of this model is 79.6 (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 | 32% |
| 70 to 90 | Confident: backbone generally right | 49% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 11% |
What pLDDT means and how to read it
DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. In a complex with DNA polymerase alpha (DNA polymerase alpha:primase) constitutes a replicative polymerase. Both primase components participate in formation of the active center, but the ATP-binding site is exclusively located on p48
DNA polymerase alpha:primase is a four subunit enzyme complex, which is assembled throughout the cell cycle, and consists of the two DNA polymerase subunits A POL1 and B POL12, and the DNA primase large PRI2 and small PRI1 subunits (PubMed:3061469). Interacts with MCM10 (PubMed:16675460)
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6DTV | X-ray | 1.12 Å | A=316-512 |
| 6DTZ | X-ray | 1.36 Å | A=316-512 |
| 7TL2 | X-ray | 1.53 Å | A=316-512 |
| 3LGB | X-ray | 1.54 Å | A/B=317-512 |
| 7TL4 | X-ray | 1.8 Å | A=316-512 |
| 6DU0 | X-ray | 1.82 Å | A=316-512 |
| 7TL3 | X-ray | 2.07 Å | A=316-512 |
| 8B9A | EM | 3.5 Å | A=1-528 |
| 8B9B | EM | 3.5 Å | A=1-528 |
| 8FOK | EM | 3.56 Å | B=1-528 |
| 8FOC | EM | 3.7 Å | B=1-528 |
| 8FOD | EM | 3.8 Å | B=1-528 |
| 8B9C | EM | 4.6 Å | A=1-528 |
| 8FOJ | EM | 4.8 Å | B=1-528 |
| 8FOH | EM | 4.93 Å | B=1-528 |
| 8FOE | EM | 5.6 Å | B=1-528 |
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