Ubiquitin carboxyl-terminal hydrolase BAP1 (BAP1) is a 729-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q92560.
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The mean pLDDT of this model is 62.9 (low 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 | 31% |
| 70 to 90 | Confident: backbone generally right | 13% |
| 50 to 70 | Low: treat with caution | 10% |
| Below 50 | Very low: often disordered regions | 47% |
What pLDDT means and how to read it
Deubiquitinating enzyme that plays a key role in chromatin by mediating deubiquitination of histone H2A and HCFC1 (PubMed:12485996, PubMed:18757409, PubMed:20436459, PubMed:25451922, PubMed:35051358). Catalytic component of the polycomb repressive deubiquitinase (PR-DUB) complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-120' (H2AK119ub1) (PubMed:20436459, PubMed:25451922, PubMed:30664650, PubMed:35051358). Does not deubiquitinate monoubiquitinated histone H2B (PubMed:20436459, PubMed:30664650). The PR-DUB complex is an epigenetic regulator of gene expression and acts as a transcriptional coactivator, affecting genes involved in…
Core component of the polycomb repressive deubiquitinase (PR-DUB) complex, at least composed of BAP1, one of ASXL1, ASXL2 or (probably) ASXL3, and one of MBD5 or MBD6 (PubMed:20436459, PubMed:24634419, PubMed:30664650, PubMed:36180891). The PR-DUB core associates with a number of accessory proteins, including FOXK1, FOXK2, KDM1B, HCFC1, YY1 and OGT; KDM1B specifically associates with ASXL2…
Cytoplasm, Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8H1T | EM | 3.0 Å | L=1-729 |
| 9U5U | EM | 3.12 Å | L=5-715 |
| 8SVF | EM | 3.2 Å | K=1-729 |
| 7VPW | X-ray | 3.76 Å | B=706-724 |
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