Bifunctional polynucleotide phosphatase/kinase (PNKP) is a 521-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q96T60.
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The mean pLDDT of this model is 90.9 (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 | 83% |
| 70 to 90 | Confident: backbone generally right | 9% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 7% |
What pLDDT means and how to read it
Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways (PubMed:10446192, PubMed:10446193, PubMed:15385968, PubMed:20852255, PubMed:28453785). Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone (PubMed:10446192, PubMed:10446193)
Monomer (By similarity). Interacts (via FHA domain) with XRCC4; mainly interacts with XRCC4 phosphorylated by CK2 but is also able to interact at much lower level with unphosphorylated PNKP (PubMed:15385968, PubMed:20852255, PubMed:28453785)
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
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