Apoptotic protease-activating factor 1 (APAF1) is a 1248-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O14727.
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The mean pLDDT of this model is 85.4 (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 | 36% |
| 70 to 90 | Confident: backbone generally right | 58% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis
Monomer. Oligomerizes to a heptameric ring, known as the apoptosome, upon binding of cytochrome c and dATP. Oligomeric Apaf-1 and pro-caspase-9 bind to each other via their respective NH2-terminal CARD domains and consecutively mature caspase-9 is released from the complex. Pro-caspase-3 is recruited into the Apaf-1-pro-caspase-9 complex via interaction with pro-caspase-9. Interacts with APIP.…
Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1CY5 | X-ray | 1.3 Å | A=1-97 |
| 2P1H | X-ray | 1.59 Å | A=1-92 |
| 2YGS | X-ray | 1.6 Å | A=1-92 |
| 4RHW | X-ray | 2.1 Å | A/B/C/D=1-97 |
| 1Z6T | X-ray | 2.21 Å | A/B/C/D=1-591 |
| 3YGS | X-ray | 2.5 Å | C=1-95 |
| 8XQK | X-ray | 2.85 Å | A/B/C/D=1-97 |
| 5WVC | X-ray | 2.99 Å | A/C/E=1-95 |
| 3JBT | EM | 3.8 Å | A/C/E/G/I/K/M=1-1248 |
| 5JUY | EM | 4.1 Å | A/B/C/D/E/F/G=1-1248 |
| 5WVE | EM | 4.4 Å | A/C/E/G/I/K/M=1-1248, O/P/Q/R/W/X=1-102 |
| 3J2T | EM | 9.5 Å | A/B/C/D/E/F/G=1-1248 |
| 1C15 | NMR | A=1-97 | |
| 1CWW | NMR | A=1-97 |
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