Cysteine protease ATG4B (ATG4B) is a 393-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9Y4P1.
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The mean pLDDT of this model is 86.2 (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 | 70% |
| 70 to 90 | Confident: backbone generally right | 11% |
| 50 to 70 | Low: treat with caution | 9% |
| Below 50 | Very low: often disordered regions | 10% |
What pLDDT means and how to read it
Cysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins (PubMed:15169837, PubMed:15187094, PubMed:17347651, PubMed:19322194, PubMed:21177865, PubMed:22302004, PubMed:26378241, PubMed:27527864, PubMed:28633005, PubMed:28821708, PubMed:29232556, PubMed:30076329, PubMed:30443548, PubMed:30661429). Required for canonical autophagy (macroautophagy), non-canonical autophagy as well as for mitophagy (PubMed:33773106, PubMed:33909989). The protease activity is required for proteolytic activation of ATG8 family proteins: cleaves the C-terminal amino acid of ATG8 proteins MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAPL1, GABARAPL2…
Interacts with PFKP; promoting phosphorylation of ATG4B at Ser-34 (PubMed:33607258). Interacts with GBP7 (By similarity)
Cytoplasm, Cytoplasm, cytosol, Cytoplasmic vesicle, autophagosome, Endoplasmic reticulum, Mitochondrion
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5LXI | X-ray | 1.44 Å | C/E=384-393 |
| 5LXH | X-ray | 1.58 Å | E/F/G=384-393 |
| 2CY7 | X-ray | 1.9 Å | A=1-393 |
| 2Z0D | X-ray | 1.9 Å | A=1-353 |
| 2Z0E | X-ray | 1.9 Å | A=1-353 |
| 2D1I | X-ray | 2.0 Å | A/B=1-393 |
| 2ZZP | X-ray | 2.05 Å | A=1-353 |
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