Caspase-9 (CASP9) is a 416-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P55211.
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The mean pLDDT of this model is 80.3 (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 | 53% |
| 70 to 90 | Confident: backbone generally right | 26% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 18% |
What pLDDT means and how to read it
Involved in the activation cascade of caspases responsible for apoptosis execution. Binding of caspase-9 to Apaf-1 leads to activation of the protease which then cleaves and activates effector caspases caspase-3 (CASP3) or caspase-7 (CASP7). Promotes DNA damage-induced apoptosis in a ABL1/c-Abl-dependent manner. Proteolytically cleaves poly(ADP-ribose) polymerase (PARP). Cleaves BIRC6 following inhibition of BIRC6-caspase binding by DIABLO/SMAC (PubMed:36758105, PubMed:36758106)
Heterotetramer that consists of two anti-parallel arranged heterodimers, each one formed by a 35 kDa (p35) and a 10 kDa (p10) subunit. Caspase-9 and APAF1 bind to each other via their respective NH2-terminal CED-3 homologous domains in the presence of cytochrome C and ATP. Interacts (inactive form) with EFHD2. Interacts with HAX1. Interacts with BIRC2/c-IAP1, XIAP/BIRC4, BIRC5/survivin,…
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3D9T | X-ray | 1.5 Å | C/D=316-321 |
| 4RHW | X-ray | 2.1 Å | E/F=1-100 |
| 1NW9 | X-ray | 2.4 Å | B=140-416 |
| 3YGS | X-ray | 2.5 Å | P=1-95 |
| 1JXQ | X-ray | 2.8 Å | A/B/C/D=139-416 |
| 2AR9 | X-ray | 2.8 Å | A/B/C/D=139-416 |
| 5WVC | X-ray | 2.99 Å | B/D/F=1-128 |
| 3V3K | X-ray | 3.49 Å | A/C/E/G/I/K/M/O=141-416 |
| 5JUY | EM | 4.1 Å | O/P/Q/R=1-95 |
| 5WVE | EM | 4.4 Å | S/T/U/V/Y=1-100 |
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