Phosphoglycerate kinase (PGK1) is a 416-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P00560.
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The mean pLDDT of this model is 96.7 (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 | 95% |
| 70 to 90 | Confident: backbone generally right | 5% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Catalyzes one of the two ATP producing reactions in the glycolytic pathway via the reversible conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate (PubMed:6254992). Both L- and D- forms of purine and pyrimidine nucleotides can be used as substrates, but the activity is much lower on pyrimidines (By similarity). Negatively regulates the biosynthesis of acetyl-CoA from pyruvate in the mitochondrion (By similarity)
Monomer
Cytoplasm, Mitochondrion
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1FW8 | X-ray | 2.3 Å | A=74-416 |
| 1QPG | X-ray | 2.4 Å | A=2-416 |
| 3PGK | X-ray | 2.5 Å | A=2-416 |
| 9R9O | EM | 2.9 Å | B=2-66 |
| 9R9P | EM | 3.0 Å | B=2-66 |
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