Polyubiquitin (UBI4) is a 381-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0CG63.
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The mean pLDDT of this model is 92.1 (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 | 79% |
| 70 to 90 | Confident: backbone generally right | 17% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked…
Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4Q5E | X-ray | 1.87 Å | B=305-380 |
| 4Q5H | X-ray | 2.0 Å | B=305-380 |
| 4NNJ | X-ray | 2.4 Å | B/D/E=305-380 |
| 3OLM | X-ray | 2.5 Å | D=305-380 |
| 4HCN | X-ray | 2.6 Å | B=305-380 |
| 3CMM | X-ray | 2.7 Å | B/D=305-380 |
| 3L0W | X-ray | 2.8 Å | B=1-76 |
| 3L10 | X-ray | 2.8 Å | B=1-76 |
| 9OFV | EM | 3.16 Å | H/J/K=305-380 |
| 8DAV | EM | 3.5 Å | I/J/K=305-380 |
| 8DAW | EM | 3.6 Å | I/J/K/L=305-380 |
| 8DAU | EM | 3.7 Å | I/J/K=305-380 |
| 8DAT | EM | 3.8 Å | J/K/L=305-380 |
| 1OTR | NMR | B=305-380 | |
| 1Q0W | NMR | B=305-380 | |
| 1WR1 | NMR | A=305-380 | |
| 1ZW7 | NMR | A=229-304 | |
| 2G3Q | NMR | B=305-380 | |
| 2JT4 | NMR | B=305-380 | |
| 2JWZ | NMR | A=305-380 |
Showing 20 of 22 experimental structures (best resolution first).
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