V-type proton ATPase subunit C (VMA5) is a 392-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P31412.
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The mean pLDDT of this model is 89.5 (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 | 72% |
| 70 to 90 | Confident: backbone generally right | 19% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 5% |
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:10781598, PubMed:11777935, PubMed:1730668, PubMed:8416931). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments (PubMed:8416931). Subunit C is necessary for the assembly of the catalytic sector of the enzyme and is likely to have a specific function in its catalytic activity (PubMed:15792803). Reversibly leaves the enzyme after glucose depletion, causing the catalytic subcomplex V1 to detach from the V0 section (PubMed:15792803)
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:25971514). Interacts directly with VMA4 (PubMed:15751969)
Vacuole membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1U7L | X-ray | 1.75 Å | A=1-392 |
| 4EFA | X-ray | 2.82 Å | C=158-277 |
| 4DL0 | X-ray | 2.9 Å | C/I=158-277 |
| 7TMM | EM | 3.5 Å | O=1-392 |
| 7TMR | EM | 3.5 Å | O=1-392 |
| 7FDE | EM | 3.8 Å | O=1-392 |
| 7FDA | EM | 4.2 Å | O=1-392 |
| 7FDB | EM | 4.8 Å | O=1-392 |
| 6O7V | EM | 6.6 Å | O=1-392 |
| 7FDC | EM | 6.6 Å | O=1-392 |
| 5VOX | EM | 6.8 Å | O=1-392 |
| 3J9T | EM | 6.9 Å | O=1-392 |
| 6O7W | EM | 7.0 Å | O=1-392 |
| 3J9U | EM | 7.6 Å | O=1-392 |
| 5VOZ | EM | 7.6 Å | O=1-392 |
| 5VOY | EM | 7.9 Å | O=1-392 |
| 3J9V | EM | 8.3 Å | O=1-392 |
| 6O7X | EM | 8.7 Å | O=1-392 |
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