Periplasmic serine endoprotease DegP (degP) is a 474-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0C0V0.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 85.2 (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 | 59% |
| 70 to 90 | Confident: backbone generally right | 23% |
| 50 to 70 | Low: treat with caution | 13% |
| Below 50 | Very low: often disordered regions | 6% |
What pLDDT means and how to read it
DegP acts as a chaperone at low temperatures but switches to a peptidase (heat shock protein) at higher temperatures (PubMed:10319814). Degrades transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions (PubMed:16303867). DegP is efficient with Val-Xaa and Ile-Xaa peptide bonds, suggesting a preference for beta-branched side chain amino acids (PubMed:8830688). Only unfolded proteins devoid of disulfide bonds appear capable of being cleaved, thereby preventing non-specific proteolysis of folded proteins (PubMed:8830688). Its proteolytic activity is essential for the survival of cells at elevated temperatures…
DegP can reversibly switch between different oligomeric forms that represent inactive (6-mer) and active (12- and 24-mer) protease states. Substrate binding triggers the conversion of the resting DegP trimer and hexamer into catalytically active 12- and 24-mers. The conversion of 6-mer (DegP6) into 12-mer (DegP12) or 24-mer (DegP24) is crucial in regulating protease activity
Cell inner membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8F0A | EM | 2.6 Å | A/B/C=38-385, D/E/F=400-474 |
| 1KY9 | X-ray | 2.8 Å | A/B=27-474 |
| 3MH7 | X-ray | 2.96 Å | A=27-474 |
| 3CS0 | X-ray | 3.0 Å | A=27-474 |
| 3MH5 | X-ray | 3.0 Å | A/B=27-474 |
| 3OU0 | X-ray | 3.0 Å | A=27-474 |
| 3MH4 | X-ray | 3.1 Å | A/B=27-474 |
| 8F0U | EM | 3.1 Å | A=38-385, D=400-474 |
| 3MH6 | X-ray | 3.6 Å | A=27-474 |
| 6JJK | X-ray | 3.6 Å | A/B/C/D/E/F=35-474 |
| 3OTP | X-ray | 3.76 Å | A/B/C/D/E/F=27-474 |
| 6JJO | X-ray | 4.16 Å | A/B/C/D/E/F=27-474 |
| 6JJL | X-ray | 4.2 Å | A/B/C/D/E/F=35-474 |
| 8F26 | EM | 9.7 Å | A=38-385, D=400-474 |
| 8F1T | EM | 12.1 Å | A/B/C=38-385, D/E/F=400-474 |
| 8F1U | EM | 13.8 Å | A/B/C=38-385, D/E/F=400-474 |
| 8F21 | EM | 14.1 Å | A/B/C=38-385, D/E/F=400-474 |
| 2ZLE | EM | 28.0 Å | A/B/C/E/F/G/H/I/J/K/L/M=27-474 |
| 4A8D | EM | 28.0 Å | A/B/C/D/E/F/G/H/I/J/K/L=27-474 |
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