Small ribosomal subunit protein uS4 (rpsD) is a 209-residue protein from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P80373.
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The mean pLDDT of this model is 92.1 (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 | 77% |
| 70 to 90 | Confident: backbone generally right | 23% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation
Part of the 30S ribosomal subunit (PubMed:11007480, PubMed:11014182, PubMed:11014183, PubMed:11163189, PubMed:11228145, PubMed:11283358, PubMed:11296217, PubMed:11340196, PubMed:11511350, PubMed:11866529, PubMed:25775268, PubMed:26792896). Contacts protein S5 (PubMed:11340196). The interaction surface between S4 and S5 is involved in control of translational fidelity
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9NO7 | EM | 2.13 Å | d=1-209 |
| 4Y4O | X-ray | 2.3 Å | 1d/2d=1-209 |
| 8CVL | X-ray | 2.3 Å | 1d/2d=1-209 |
| 8FC6 | X-ray | 2.35 Å | 1d/2d=1-209 |
| 8VTW | X-ray | 2.35 Å | 1d/2d=1-209 |
| 4W2F | X-ray | 2.4 Å | AD/CD=1-209 |
| 6XHV | X-ray | 2.4 Å | 1d/2d=1-209 |
| 7RQA | X-ray | 2.4 Å | 1d/2d=1-209 |
| 7RQE | X-ray | 2.4 Å | 1d/2d=1-209 |
| 8CVJ | X-ray | 2.4 Å | 1d/2d=1-209 |
| 8VTU | X-ray | 2.4 Å | 1d/2d=1-209 |
| 8VTX | X-ray | 2.4 Å | 1d/2d=1-209 |
| 9MTP | X-ray | 2.4 Å | 1d/2d=1-209 |
| 10PX | X-ray | 2.45 Å | 1d/2d=1-209 |
| 7RQB | X-ray | 2.45 Å | 1d/2d=1-209 |
| 8FC4 | X-ray | 2.45 Å | 1d/2d=1-209 |
| 8G2A | X-ray | 2.45 Å | 1d/2d=1-209 |
| 9D0I | X-ray | 2.45 Å | 1d/2d=1-209 |
| 2VQE | X-ray | 2.5 Å | D=1-209 |
| 4Y4P | X-ray | 2.5 Å | 1d/2d=1-209 |
Showing 20 of 413 experimental structures (best resolution first).
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