Ribonuclease HI (rnhA) is a 155-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0A7Y4.
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The mean pLDDT of this model is 95.6 (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 | 92% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer. Involved in production of retron derived msDNA (a branched RNA linked by a 2',5'-phosphodiester bond to a single-stranded DNA). Strain K12 / MG1655 does not have retrons, however they can be expressed in this strain which requires this enzyme…
Monomer
Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1JL1 | X-ray | 1.3 Å | A=1-155 |
| 1F21 | X-ray | 1.4 Å | A=1-155 |
| 2YV0 | X-ray | 1.4 Å | X=1-155 |
| 3QIO | X-ray | 1.4 Å | A=79-103 |
| 2RN2 | X-ray | 1.48 Å | A=1-155 |
| 1JXB | X-ray | 1.6 Å | A=1-155 |
| 3HYF | X-ray | 1.7 Å | A=79-103 |
| 3QIN | X-ray | 1.7 Å | A=79-103 |
| 7VSD | X-ray | 1.7 Å | A/B=1-155 |
| 1JL2 | X-ray | 1.76 Å | A/B/C/D=1-49, A/B/C/D=125-155 |
| 7VSA | X-ray | 1.76 Å | A/B=1-155 |
| 3AA4 | X-ray | 1.79 Å | A=1-155 |
| 1KVA | X-ray | 1.8 Å | A=1-155 |
| 1LAV | X-ray | 1.8 Å | A=1-155 |
| 1LAW | X-ray | 1.8 Å | A=1-155 |
| 1RBR | X-ray | 1.8 Å | A=1-155 |
| 1RBS | X-ray | 1.8 Å | A=1-155 |
| 1RBT | X-ray | 1.8 Å | A=1-155 |
| 1RBU | X-ray | 1.8 Å | A=1-155 |
| 1RBV | X-ray | 1.8 Å | A=1-155 |
Showing 20 of 49 experimental structures (best resolution first).
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