Interstitial collagenase (MMP1) is a 469-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P03956.
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The mean pLDDT of this model is 91.3 (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 | 85% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 6% |
| Below 50 | Very low: often disordered regions | 5% |
What pLDDT means and how to read it
Cleaves collagens of types I, II, and III at one site in the helical domain. Also cleaves collagens of types VII and X (PubMed:1645757, PubMed:2153297, PubMed:2557822). In case of HIV infection, interacts and cleaves the secreted viral Tat protein, leading to a decrease in neuronal Tat's mediated neurotoxicity (PubMed:16807369)
(Microbial infection) Interacts with HIV-1 Tat
Secreted, extracellular space, extracellular matrix
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1HFC | X-ray | 1.5 Å | A=101-269 |
| 1CGE | X-ray | 1.9 Å | A=102-269 |
| 966C | X-ray | 1.9 Å | A=108-264 |
| 1CGF | X-ray | 2.1 Å | A/B=102-263 |
| 1SU3 | X-ray | 2.2 Å | A/B=20-469 |
| 2TCL | X-ray | 2.2 Å | A=101-269 |
| 3SHI | X-ray | 2.2 Å | A/G/M=106-261 |
| 1CGL | X-ray | 2.4 Å | A/B=101-269 |
| 2J0T | X-ray | 2.54 Å | A/B/C=101-269 |
| 2CLT | X-ray | 2.67 Å | A/B=100-466 |
| 4AUO | X-ray | 3.0 Å | A/B=100-466 |
| 1AYK | NMR | A=101-269 | |
| 2AYK | NMR | A=101-269 | |
| 3AYK | NMR | A=101-269 | |
| 4AYK | NMR | A=101-269 |
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