Dipeptidyl aminopeptidase BII (dapb2) is a 722-residue protein from Pseudoxanthomonas mexicana. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: V5YM14.
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The mean pLDDT of this model is 95.3 (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 | 4% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
Exopeptidase that catalyzes the removal of dipeptide units (NH2-P2-P1-) from the free amino termini of oligopeptides and small proteins (PubMed:24598890, PubMed:24827749, PubMed:8892831). Peptide digestion is sequential and substrate recognition is non-specific, with the exception that Pro is not suitable as a P1 residue (PubMed:24827749). Removes many residues of bioactive oligopeptides such as angiotensin I and neuromedin N and also cleaves oxidized insulin B chain. Able to hydrolyze an X-Pro bond, an imido bond. No endopeptidase activity (PubMed:8892831). May play a physiological role in feeding (PubMed:24598890)
Homodimer
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3WOL | X-ray | 1.74 Å | A/B=25-722 |
| 3WON | X-ray | 1.75 Å | A/B=25-722 |
| 3WOO | X-ray | 1.8 Å | A/B=25-722 |
| 3WOQ | X-ray | 1.82 Å | A/B=25-722 |
| 3WOM | X-ray | 1.86 Å | A/B=25-722 |
| 3WOK | X-ray | 1.95 Å | A/B=25-722 |
| 3WOP | X-ray | 1.95 Å | A/B=25-722 |
| 3WOI | X-ray | 2.1 Å | A/B=25-722 |
| 3WOR | X-ray | 2.1 Å | A/B=25-722 |
| 4Y06 | X-ray | 2.18 Å | A/B=1-722 |
| 3WOJ | X-ray | 2.2 Å | A/B=25-722 |
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