Exodeoxyribonuclease I (sbcB) is a 475-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P04995.
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The mean pLDDT of this model is 95.9 (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 | 92% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Degrades single-stranded DNA (ssDNA) in a highly processive manner (PubMed:23609540). Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage of DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease or AP lyase (PubMed:1329027)
Monomer (PubMed:23609540). Interacts with ssb (via C-terminus); this interaction stimulates the exonuclease activity by recruiting the enzyme to its substrate (PubMed:18591666, PubMed:20018747)
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2QXF | X-ray | 1.5 Å | A=1-475 |
| 3HL8 | X-ray | 1.55 Å | A=1-475 |
| 3HP9 | X-ray | 1.6 Å | A=1-475 |
| 3C95 | X-ray | 1.7 Å | A=1-475 |
| 4JRP | X-ray | 1.95 Å | A/B=1-475 |
| 4HCB | X-ray | 2.0 Å | A/B=1-475 |
| 1FXX | X-ray | 2.4 Å | A=1-475 |
| 3C94 | X-ray | 2.7 Å | A=1-475 |
| 4HCC | X-ray | 2.96 Å | A/B=1-475 |
| 4JRQ | X-ray | 3.0 Å | A/B=1-475 |
| 4JS4 | X-ray | 3.1 Å | A/B=1-475 |
| 4JS5 | X-ray | 3.5 Å | A/B=1-475 |
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