Ubiquitin carboxyl-terminal hydrolase RPN11 (RPN11) is a 306-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P43588.
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The mean pLDDT of this model is 81.9 (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 | 39% |
| 70 to 90 | Confident: backbone generally right | 44% |
| 50 to 70 | Low: treat with caution | 11% |
| Below 50 | Very low: often disordered regions | 6% |
What pLDDT means and how to read it
Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. RPN11 is the only catalytically active member of the lid and serves as the essential deubiquitinase of the proteasome
Component of the lid subcomplex of the 19S proteasome regulatory particle complex (also named PA700 complex). The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. Interacts directly with RPN8 and STS1
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5W83 | X-ray | 1.55 Å | B=1-222 |
| 4O8Y | X-ray | 1.95 Å | B=2-239 |
| 4O8X | X-ray | 1.99 Å | B=2-239 |
| 4OCM | X-ray | 1.99 Å | B/E=1-220 |
| 4OCN | X-ray | 2.25 Å | B/E=1-220 |
| 4OWP | X-ray | 2.35 Å | B=2-229 |
| 4OCL | X-ray | 2.4 Å | B/E=1-220 |
| 5U4P | X-ray | 2.5 Å | B=2-219 |
| 3JCK | EM | 3.5 Å | G=1-306 |
| 9CGC | EM | 3.61 Å | V=1-306 |
| 6J2Q | EM | 3.8 Å | V=1-306 |
| 6J2X | EM | 3.8 Å | V=1-306 |
| 5MPD | EM | 4.1 Å | V=1-306 |
| 6FVT | EM | 4.1 Å | V=18-306 |
| 6EF3 | EM | 4.17 Å | r=1-306 |
| 5WVK | EM | 4.2 Å | V=1-306 |
| 5MPE | EM | 4.5 Å | V=1-306 |
| 6FVU | EM | 4.5 Å | V=18-306 |
| 6FVW | EM | 4.5 Å | V=18-306 |
| 6J30 | EM | 4.5 Å | V=1-306 |
Showing 20 of 38 experimental structures (best resolution first).
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