Pleckstrin homology domain-containing family M member 1 (PLEKHM1) is a 1056-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9Y4G2.
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The mean pLDDT of this model is 65.8 (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 | 27% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 37% |
What pLDDT means and how to read it
Acts as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. Acts as a dual effector of RAB7A and ARL8B that simultaneously binds these GTPases, bringing about clustering and fusion of late endosomes and lysosomes (PubMed:25498145, PubMed:28325809). Required for late stages of endolysosomal maturation, facilitating both endocytosis-mediated degradation of growth factor receptors and autophagosome clearance. Interaction with Arl8b is a crucial factor in the terminal maturation of autophagosomes and to mediate autophagosome-lysosome fusion…
Interacts (via N- and C-terminus) with RAB7A (GTP-bound form) (PubMed:20943950, PubMed:25500191, PubMed:28325809). Simultaneously interacts with RAB7A and ARL8B; bringing about clustering and fusion of late endosomes and lysosomes (PubMed:28325809). Interacts (via RUN domain) with ARL8B (GTP-bound form); the interaction is required for PLEKHM1 localization to lysosomes and for ARL8B function in…
Autolysosome membrane, Endosome membrane, Late endosome membrane, Lysosome membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5DPS | X-ray | 2.0 Å | A/B/C=627-638 |
| 8JC5 | X-ray | 2.01 Å | C/D=10-205 |
| 5DPW | X-ray | 2.19 Å | B/D/F/H/J/L/N/P=629-642 |
| 5DPR | X-ray | 2.5 Å | A/B/C/D=627-638 |
| 5DPT | X-ray | 2.9 Å | A/B=627-638 |
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