Collagenase 3 (MMP13) is a 471-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P45452.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 88.6 (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 | 75% |
| 70 to 90 | Confident: backbone generally right | 14% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Plays a role in the degradation of extracellular matrix proteins including fibrillar collagen, fibronectin, TNC and ACAN. Cleaves triple helical collagens, including type I, type II and type III collagen, but has the highest activity with soluble type II collagen. Can also degrade collagen type IV, type XIV and type X. May also function by activating or degrading key regulatory proteins, such as TGFB1 and CCN2. Plays a role in wound healing, tissue remodeling, cartilage degradation, bone development, bone mineralization and ossification. Required for normal embryonic bone development and ossification. Plays a role in the healing of bone fractures via endochondral ossification. Plays a role…
Monomer. Interacts with TIMP1, TIMP2 and TIMP3. Binds (via the C-terminal region) to collagen
Secreted, extracellular space, extracellular matrix, Secreted
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5B5O | X-ray | 1.2 Å | A/B=103-274 |
| 3ZXH | X-ray | 1.3 Å | A/B=104-274 |
| 4JP4 | X-ray | 1.43 Å | A/B=103-274 |
| 3WV3 | X-ray | 1.6 Å | A/B=104-274 |
| 5B5P | X-ray | 1.6 Å | A/B=103-274 |
| 5UWK | X-ray | 1.6 Å | A/B=104-274 |
| 830C | X-ray | 1.6 Å | A/B=104-271 |
| 5UWM | X-ray | 1.62 Å | A/B=104-274 |
| 4L19 | X-ray | 1.66 Å | A/B=104-274 |
| 1XUC | X-ray | 1.7 Å | A/B=104-274 |
| 2YIG | X-ray | 1.7 Å | A/B=104-274 |
| 6HV2 | X-ray | 1.71 Å | A=103-270, B=163-167 |
| 2OW9 | X-ray | 1.74 Å | A/B=104-270 |
| 5BPA | X-ray | 1.79 Å | A/B=104-274 |
| 1XUD | X-ray | 1.8 Å | A/B=104-274 |
| 1XUR | X-ray | 1.85 Å | A/B=104-274 |
| 5BOT | X-ray | 1.85 Å | A/B=104-274 |
| 3ELM | X-ray | 1.9 Å | A/B=104-274 |
| 3KRY | X-ray | 1.9 Å | A/B/C/D=104-267 |
| 3O2X | X-ray | 1.9 Å | A/B/C/D=105-267 |
Showing 20 of 49 experimental structures (best resolution first).
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.