Ras-related protein Rab-5A (RAB5A) is a 215-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P20339.
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The mean pLDDT of this model is 84.9 (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 | 69% |
| 70 to 90 | Confident: backbone generally right | 9% |
| 50 to 70 | Low: treat with caution | 7% |
| Below 50 | Very low: often disordered regions | 15% |
What pLDDT means and how to read it
The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. RAB5A is required for the fusion of plasma membranes and early endosomes and involved in early endocytic trafficking (PubMed:10818110, PubMed:14617813, PubMed:15378032, PubMed:16086013, PubMed:16410077, PubMed:17562788). Required for EEA1 recruitment to early endosomes (PubMed:16086013, PubMed:17562788). Recruits…
Interacts (GTP-bound) with SGSM3; SGSM3 acts as a GAP (PubMed:17562788). Interacts with SGSM1 (By similarity). Interacts with GDI1; this promotes dissociation from membranes; phosphorylation at Ser-84 disrupts this interaction (PubMed:23815289, PubMed:29125462). Interacts with GDI2; phosphorylation at Ser-84 disrupts the interaction (PubMed:29125462). Interacts (GTP-bound) with EEA1; EEA1 acts…
Cell membrane, Early endosome membrane, Melanosome, Cytoplasmic vesicle, Cell projection, ruffle, Membrane, Cytoplasm, cytosol, Cytoplasmic vesicle, phagosome membrane, Endosome membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1R2Q | X-ray | 1.05 Å | A=15-184 |
| 1N6H | X-ray | 1.51 Å | A=15-184 |
| 1N6P | X-ray | 1.54 Å | A=15-184 |
| 1N6K | X-ray | 1.55 Å | A=15-184 |
| 1N6R | X-ray | 1.55 Å | A=15-184 |
| 1N6I | X-ray | 1.6 Å | A=15-184 |
| 1N6L | X-ray | 1.6 Å | A=15-184 |
| 1N6N | X-ray | 1.6 Å | A=15-184 |
| 1N6O | X-ray | 1.8 Å | A=15-184 |
| 3MJH | X-ray | 2.03 Å | A/C=16-183 |
| 1TU4 | X-ray | 2.2 Å | A/B/C/D=14-184 |
| 1TU3 | X-ray | 2.31 Å | A/B/C/D/E=14-184 |
| 4Q9U | X-ray | 4.62 Å | B/F=15-184 |
| 7BL1 | EM | 9.8 Å | DDD=16-183 |
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