V-type proton ATPase subunit E (VMA4) is a 233-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P22203.
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The mean pLDDT of this model is 90.1 (very high 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 | 29% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:8416931). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments (PubMed:2145285, PubMed:8416931)
Homodimer (PubMed:8626613). V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (components A to H) attached to an integral membrane V0 proton pore complex (components: a, c, c', c'', d, e, f and VOA1) (PubMed:18055462, PubMed:2145285, PubMed:25971514, PubMed:27295975, PubMed:8416931). Interacts with VMA5; the interaction is direct (PubMed:15751969). Interacts…
Vacuole membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9COP | EM | 2.7 Å | I/K=1-233 |
| 4EFA | X-ray | 2.82 Å | E=1-233 |
| 4DL0 | X-ray | 2.9 Å | E/J=1-233 |
| 7TMO | EM | 3.3 Å | G/I/K=1-233 |
| 7TMP | EM | 3.3 Å | G/I/K=1-233 |
| 7TMQ | EM | 3.3 Å | G/I/K=1-233 |
| 7TMM | EM | 3.5 Å | G/I/K=1-233 |
| 7TMR | EM | 3.5 Å | G/I/K=1-233 |
| 7FDE | EM | 3.8 Å | G/I/K=1-233 |
| 7FDA | EM | 4.2 Å | G/I/K=1-233 |
| 7FDB | EM | 4.8 Å | G/I/K=1-233 |
| 5D80 | X-ray | 6.2 Å | I/K/M/i/k/m=1-233 |
| 6O7V | EM | 6.6 Å | G/I/K=1-233 |
| 7FDC | EM | 6.6 Å | G/I/K=1-233 |
| 5VOX | EM | 6.8 Å | G/I/K=1-233 |
| 3J9T | EM | 6.9 Å | G/I/K=1-233 |
| 5BW9 | X-ray | 7.0 Å | I/K/M/i/k/m=1-233 |
| 6O7W | EM | 7.0 Å | G/I/K=1-233 |
| 3J9U | EM | 7.6 Å | G/I/K=1-233 |
| 5VOZ | EM | 7.6 Å | G/I/K=1-233 |
Showing 20 of 24 experimental structures (best resolution first).
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