Ubiquitin carboxyl-terminal hydrolase 4 (USP4) is a 963-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q13107.
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The mean pLDDT of this model is 75.9 (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 | 35% |
| 70 to 90 | Confident: backbone generally right | 37% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 19% |
What pLDDT means and how to read it
Deubiquitinating enzyme that removes conjugated ubiquitin from target proteins (PubMed:16316627, PubMed:16339847, PubMed:16472766, PubMed:20595234, PubMed:22347420, PubMed:25404403, PubMed:28604766, PubMed:30514904). Deubiquitinates PDPK1 (PubMed:22347420). Deubiquitinates TRIM21 (PubMed:16316627). Deubiquitinates receptor ADORA2A which increases the amount of functional receptor at the cell surface (PubMed:16339847). Deubiquitinates HAS2 (PubMed:28604766). Deubiquitinates MAVs leading to maintain MAVS protein stability, resulting in increased production of type I interferons (IFN-I) and enhanced antiviral innate immune responses against viral infections (PubMed:39589880). Deubiquitinates…
Interacts with RB1 (both dephosphorylated and hypophosphorylated forms) (PubMed:11571652). Interacts with RBL1 and RBL2 (By similarity). Interacts with ADORA2A (via cytoplasmic C-terminus); the interaction is direct (PubMed:16339847). Interacts with SART3; recruits USP4 to its substrate PRPF3 (PubMed:20595234)
Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2Y6E | X-ray | 2.4 Å | A/B/C/D/E/F=296-490, A/B/C/D/E/F=765-932 |
| 5CTR | X-ray | 3.01 Å | C/D=1-230 |
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