DNA primase small subunit (PRIM1) is a 420-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P49642.
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The mean pLDDT of this model is 92.7 (very high 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 | 84% |
| 70 to 90 | Confident: backbone generally right | 10% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Catalytic subunit of the DNA primase complex and component of the DNA polymerase alpha complex (also known as the alpha DNA polymerase-primase complex - primosome/replisome) which play an essential role in the initiation of DNA synthesis (PubMed:17893144, PubMed:24043831, PubMed:25550159, PubMed:26975377, PubMed:31479243, PubMed:33060134, PubMed:9268648, PubMed:9705292). During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1, an accessory subunit POLA2 and two primase subunits, the catalytic subunit PRIM1 and the regulatory subunit PRIM2) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1 (By…
Heterodimer of a catalytic subunit PRIM1 and a regulatory subunit PRIM2, also known as the DNA primase complex (PubMed:17893144, PubMed:9705292). Interacts with PRIM2 (via C-terminus) (PubMed:17893144). Component of the alpha DNA polymerase complex (also known as the alpha DNA polymerase-primase complex) consisting of four subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and…
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6RB4 | X-ray | 1.5 Å | A=1-407 |
| 4LIK | X-ray | 1.7 Å | A=1-408 |
| 6R5E | X-ray | 1.85 Å | A/E=1-407 |
| 6R5D | X-ray | 1.95 Å | A/E=1-407 |
| 4MHQ | X-ray | 2.2 Å | A=1-420 |
| 6R4U | X-ray | 2.2 Å | A/E=1-407 |
| 6R4T | X-ray | 2.35 Å | A/D=1-407 |
| 4LIL | X-ray | 2.6 Å | A=1-408 |
| 4RR2 | X-ray | 2.65 Å | A/C=1-420 |
| 4BPU | X-ray | 2.7 Å | A/C=1-420 |
| 6R4S | X-ray | 2.75 Å | A/E=1-407 |
| 8VY3 | EM | 2.98 Å | A=1-412 |
| 4BPW | X-ray | 3.0 Å | A/C=1-420 |
| 8QJ7 | EM | 3.07 Å | C=1-420 |
| 9C8V | EM | 3.39 Å | A=1-412 |
| 4BPX | X-ray | 3.4 Å | A/C=1-420 |
| 8B9D | EM | 3.4 Å | O=1-420 |
| 8D0B | EM | 3.43 Å | D=2-420 |
| 8D9D | EM | 3.59 Å | A=1-420 |
| 5EXR | X-ray | 3.6 Å | A/E=1-420 |
Showing 20 of 23 experimental structures (best resolution first).
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