DNA polymerase III subunit delta (holA) is a 343-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P28630.
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The mean pLDDT of this model is 87.8 (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 | 60% |
| 70 to 90 | Confident: backbone generally right | 33% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Part of the beta sliding clamp loading complex, which hydrolyzes ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex (PubMed:2040637). DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3'-5' exonuclease activity. The delta subunit is the wrench that will open the beta subunit dimer, which has been modeled to leave a gap large enough for ssDNA to pass through (PubMed:11525728). The gamma complex (gamma(3),delta,delta') is thought to load beta dimers onto DNA by binding ATP which alters the complex's conformation so it can bind beta sliding clamp dimers…
The DNA polymerase III holoenzyme complex contains at least 10 different subunits organized into 3 functionally essential subassemblies: the Pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The Pol III core (subunits alpha, epsilon and theta) contains the polymerase and the 3'-5' exonuclease proofreading activities (PubMed:2040637). The polymerase is…
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1JQL | X-ray | 2.5 Å | B=1-140 |
| 8GJ2 | EM | 2.6 Å | A=1-343 |
| 1JR3 | X-ray | 2.7 Å | D=1-343 |
| 8GIZ | EM | 2.7 Å | A=1-343 |
| 8GJ3 | EM | 2.8 Å | A=1-343 |
| 1JQJ | X-ray | 2.9 Å | C/D=1-343 |
| 8GJ0 | EM | 2.9 Å | A=1-343 |
| 9OYG | EM | 2.95 Å | A=1-343 |
| 8GJ1 | EM | 3.0 Å | A=1-343 |
| 8VAP | EM | 3.0 Å | A=1-333 |
| 8VAT | EM | 3.2 Å | A=1-343 |
| 3GLG | X-ray | 3.25 Å | A/F=1-343 |
| 3GLF | X-ray | 3.39 Å | A/F=1-343 |
| 1XXH | X-ray | 3.45 Å | A/F=1-343 |
| 3GLI | X-ray | 3.5 Å | A/F=1-343 |
| 8GIY | EM | 3.7 Å | A=1-343 |
| 8VAL | EM | 3.7 Å | A=1-343 |
| 8VAQ | EM | 3.8 Å | A=1-343 |
| 8VAS | EM | 3.8 Å | A=1-343 |
| 3GLH | X-ray | 3.89 Å | A/F/K=1-343 |
Showing 20 of 24 experimental structures (best resolution first).
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