E4 ubiquitin-protein ligase UFD2 (UFD2) is a 961-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P54860.
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The mean pLDDT of this model is 90.3 (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 | 68% |
| 70 to 90 | Confident: backbone generally right | 28% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
E4 ubiquitin chain-elongation enzyme specifically involved in polyubiquitin chain assembly. Binds to CDC48 and elongates mono- and diubiquitinated ERAD substrates presented by the UFD1-NPL4-CDC48/p97 (UNC) AAA ATPase complex to a chain length of 4 to 6 ubiquitin moieties. Delivers these polyubiquitinated substrates to RAD23 and DSK2, which target them to the proteasome. Has E3 ubiquitin-protein ligase activity, accepting ubiquitin from its cognate E2 ubiquitin-conjugating enzyme UBC4. Enhances ubiquitination at 'Lys-48', but not at 'Lys-29' of the Ub moiety. Promotes ubiquitin chain elongation at 'Lys-48' on the DOA10 substrate PEX29. Also involved in the proteolytic processing of the…
Interacts with CDC48. Interacts with the ubiquitin-like domain of RAD23 and DSK2. Interacts with PEX29
Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3M62 | X-ray | 2.4 Å | A=1-961 |
| 3M63 | X-ray | 2.4 Å | A=1-961 |
| 2QIZ | X-ray | 2.56 Å | A=1-961 |
| 2QJ0 | X-ray | 2.65 Å | A=1-961 |
| 9M7O | EM | 4.14 Å | A=1-961 |
| 9KHS | EM | 4.31 Å | A=1-961 |
| 9KHT | EM | 4.85 Å | A/a=1-955 |
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