DNA topoisomerase 1 (TOP1) is a 765-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P11387.
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The mean pLDDT of this model is 80.4 (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 | 70% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 26% |
What pLDDT means and how to read it
Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then rotates around the intact phosphodiester bond on the opposing strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site…
Monomer. Interacts with ERCC6 (PubMed:26030138). Interacts with TPRN; TPRN interacts with a number of DNA damage response proteins, is recruited to sites of DNA damage and may play a role in DNA damage repair (PubMed:23213405)
Nucleus, nucleolus, Nucleus, nucleoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1A31 | X-ray | 2.1 Å | A=175-765 |
| 1K4T | X-ray | 2.1 Å | A=174-765 |
| 1RRJ | X-ray | 2.3 Å | A=201-765 |
| 1A35 | X-ray | 2.5 Å | A=175-765 |
| 1EJ9 | X-ray | 2.6 Å | A=203-765 |
| 1RR8 | X-ray | 2.6 Å | C=203-765 |
| 1A36 | X-ray | 2.8 Å | A=175-765 |
| 1SC7 | X-ray | 3.0 Å | A=174-765 |
| 1SEU | X-ray | 3.0 Å | A=174-765 |
| 1T8I | X-ray | 3.0 Å | A=174-765 |
| 1NH3 | X-ray | 3.1 Å | A=203-765 |
| 1TL8 | X-ray | 3.1 Å | A=174-765 |
| 1R49 | X-ray | 3.13 Å | A=174-765 |
| 1LPQ | X-ray | 3.14 Å | A=202-765 |
| 1K4S | X-ray | 3.2 Å | A=174-765 |
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