Programmed cell death protein 6 (PDCD6) is a 191-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O75340.
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The mean pLDDT of this model is 89.1 (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 | 80% |
| 70 to 90 | Confident: backbone generally right | 9% |
| 50 to 70 | Low: treat with caution | 6% |
| Below 50 | Very low: often disordered regions | 5% |
What pLDDT means and how to read it
Calcium sensor that plays a key role in processes such as endoplasmic reticulum (ER)-Golgi vesicular transport, endosomal biogenesis or membrane repair. Acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium: calcium-binding triggers exposure of apolar surface, promoting interaction with different sets of proteins thanks to 3 different hydrophobic pockets, leading to translocation to membranes (PubMed:20691033, PubMed:25667979). Involved in ER-Golgi transport by promoting the association between PDCD6IP and TSG101, thereby bridging together the ESCRT-III and ESCRT-I complexes (PubMed:19520058). Together with PEF1, acts as a…
Homodimer and heterodimer; heterodimerizes (via the EF-hand 5) with PEF1 (PubMed:11278427, PubMed:11883899, PubMed:27784779). Isoform 1 and isoform 2 self-associate; probably forming homodimers. Interacts with CPNE4 (via VWFA domain) (By similarity). Interacts with PDCD6IP; the interaction is calcium-dependent (PubMed:16957052, PubMed:18256029, PubMed:18940611, PubMed:20691033, PubMed:25667979).…
Endoplasmic reticulum membrane, Cytoplasmic vesicle, COPII-coated vesicle membrane, Cytoplasm, Nucleus, Endosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2ZND | X-ray | 1.7 Å | A=20-191 |
| 2ZNE | X-ray | 2.2 Å | A/B=24-191 |
| 5GQQ | X-ray | 2.2 Å | C/D=24-191 |
| 3WXA | X-ray | 2.36 Å | A/B=20-191 |
| 2ZN9 | X-ray | 2.4 Å | A/B=20-191 |
| 3AAJ | X-ray | 2.4 Å | A/B=24-191 |
| 2ZN8 | X-ray | 2.7 Å | A=2-191 |
| 3AAK | X-ray | 2.7 Å | A=20-191 |
| 2ZRS | X-ray | 3.1 Å | A/B/C/D/E/F/G/H=24-191 |
| 2ZRT | X-ray | 3.3 Å | A/B/C/D/E/F/G/H=24-191 |
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