Flap endonuclease 1 (FEN1) is a 380-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P39748.
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The mean pLDDT of this model is 89.6 (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 | 83% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions.…
Interacts with PCNA (PubMed:11430825, PubMed:15616578, PubMed:26760506, PubMed:9305916). Three molecules of FEN1 bind to one PCNA trimer with each molecule binding to one PCNA monomer (PubMed:15616578). PCNA stimulates the nuclease activity without altering cleavage specificity (PubMed:15616578). The C-terminal domain binds EP300; can bind simultaneously to both PCNA and EP300 (PubMed:11430825).…
Nucleus, nucleolus, Nucleus, nucleoplasm, Mitochondrion
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9RCI | X-ray | 1.66 Å | A/B=1-336 |
| 1U7B | X-ray | 1.88 Å | B=331-350 |
| 5ZOD | X-ray | 1.9 Å | A=1-333 |
| 5ZOE | X-ray | 1.95 Å | A=1-333 |
| 5E0V | X-ray | 2.07 Å | C/D=335-350 |
| 5K97 | X-ray | 2.1 Å | A=2-336 |
| 5KSE | X-ray | 2.1 Å | A=2-336 |
| 9RDI | X-ray | 2.1 Å | A/B=1-336 |
| 3Q8K | X-ray | 2.2 Å | A=2-336 |
| 5ZOF | X-ray | 2.25 Å | A=1-333 |
| 5ZOG | X-ray | 2.3 Å | A=1-333 |
| 3Q8L | X-ray | 2.32 Å | A=2-336 |
| 3UVU | X-ray | 2.38 Å | B=352-370 |
| 3Q8M | X-ray | 2.6 Å | A/B=2-336 |
| 5UM9 | X-ray | 2.81 Å | A=2-336 |
| 5FV7 | X-ray | 2.84 Å | A/B=1-336 |
| 1UL1 | X-ray | 2.9 Å | X/Y/Z=2-380 |
| 8YJL | EM | 3.51 Å | D=1-380 |
| 8YJQ | EM | 3.51 Å | D=1-380 |
| 8YJR | EM | 3.51 Å | D=1-380 |
Showing 20 of 28 experimental structures (best resolution first).
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