Programmed cell death 6-interacting protein (PDCD6IP) is a 868-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q8WUM4.
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The mean pLDDT of this model is 83.6 (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 | 67% |
| 70 to 90 | Confident: backbone generally right | 14% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 16% |
What pLDDT means and how to read it
Multifunctional protein involved in endocytosis, multivesicular body biogenesis, membrane repair, cytokinesis, apoptosis and maintenance of tight junction integrity. Class E VPS protein involved in concentration and sorting of cargo proteins of the multivesicular body (MVB) for incorporation into intralumenal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome. Binds to the phospholipid lysobisphosphatidic acid (LBPA) which is abundant in MVBs internal membranes. The MVB pathway requires the sequential function of ESCRT-O, -I,-II and -III complexes (PubMed:14739459). The ESCRT machinery also functions in topologically equivalent…
Self-associates (PubMed:14505570, PubMed:14519844). Interacts with SH3KBP1/CIN85 (By similarity). Interacts with PDCD6 in a calcium -dependent manner (PubMed:16957052, PubMed:18256029, PubMed:18940611). Interacts with TSG101 in a calcium-dependent manner; PDCD6IP homooligomerization may be required for TSG101-binding (PubMed:14505570, PubMed:14519844, PubMed:17350572, PubMed:18641129,…
Cytoplasm, cytosol, Melanosome, Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, Secreted, extracellular exosome, Cell junction, tight junction, Midbody, Midbody ring
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5WA1 | X-ray | 1.87 Å | A=1-358 |
| 5V3R | X-ray | 1.91 Å | A=1-359 |
| 3E1R | X-ray | 2.0 Å | C=797-809 |
| 3C3R | X-ray | 2.02 Å | A=1-359 |
| 3C3Q | X-ray | 2.1 Å | A=1-359 |
| 3C3O | X-ray | 2.15 Å | A=1-359 |
| 2ZNE | X-ray | 2.2 Å | C/D=799-814 |
| 6KP3 | X-ray | 2.2 Å | A=1-359 |
| 2XS1 | X-ray | 2.3 Å | A=1-698 |
| 2XS8 | X-ray | 2.5 Å | A=1-698 |
| 2OEW | X-ray | 2.55 Å | A=1-359 |
| 2R05 | X-ray | 2.55 Å | A=2-698 |
| 2OEX | X-ray | 2.58 Å | A/B=360-702 |
| 2R03 | X-ray | 2.59 Å | A=2-698 |
| 2R02 | X-ray | 2.6 Å | A=2-698 |
| 3WUV | X-ray | 2.79 Å | C/F/I/L/O/R=796-809 |
| 2OJQ | X-ray | 2.87 Å | A=360-702 |
| 2OEV | X-ray | 3.3 Å | A=1-698 |
| 4JJY | X-ray | 6.5 Å | A/B=355-708 |
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