V-type proton ATPase catalytic subunit A (VMA1) is a 1071-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P17255.
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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 | 45% |
| 70 to 90 | Confident: backbone generally right | 45% |
| 50 to 70 | Low: treat with caution | 6% |
| Below 50 | Very low: often disordered regions | 4% |
What pLDDT means and how to read it
Catalytic 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:18055462, PubMed:2139027). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments (PubMed:18055462, PubMed:2139027)
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:25971514, PubMed:27295975). Interacts with RAV1 and RAV2 components of the RAVE complex, which are essential for the stability and assembly of V-ATPase (PubMed:11283612)
Vacuole membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1GPP | X-ray | 1.35 Å | A=283-466 |
| 1DFA | X-ray | 2.0 Å | A=284-737 |
| 1EF0 | X-ray | 2.1 Å | A/B=283-741 |
| 1JVA | X-ray | 2.1 Å | A/B=273-747 |
| 1VDE | X-ray | 2.4 Å | A/B=284-737 |
| 9COP | EM | 2.7 Å | A/E=1-1071 |
| 1UM2 | X-ray | 2.9 Å | A/B=284-737, C/D=274-747 |
| 1LWT | X-ray | 3.2 Å | A=284-737 |
| 7TMO | EM | 3.3 Å | A/C/E=1-1071 |
| 7TMP | EM | 3.3 Å | A/C/E=1-1071 |
| 7TMQ | EM | 3.3 Å | A/C/E=1-1071 |
| 1LWS | X-ray | 3.5 Å | A=284-737 |
| 7TMM | EM | 3.5 Å | A/C/E=1-1071 |
| 7TMR | EM | 3.5 Å | A/C/E=1-1071 |
| 7FDE | EM | 3.8 Å | A/C/E=1-1071 |
| 7FDA | EM | 4.2 Å | A/C/E=1-1071 |
| 7FDB | EM | 4.8 Å | A/C/E=1-1071 |
| 5D80 | X-ray | 6.2 Å | A/B/C/a/b/c=1-1071 |
| 7FDC | EM | 6.6 Å | A/C/E=1-1071 |
| 5VOX | EM | 6.8 Å | A/C/E=1-1071 |
Showing 20 of 26 experimental structures (best resolution first).
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