Large ribosomal subunit protein uL4 (rplD) is a 210-residue protein from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q5SHN9.
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The mean pLDDT of this model is 92.4 (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 | 88% |
| 70 to 90 | Confident: backbone generally right | 10% |
| 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, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity)
Part of the 50S ribosomal subunit
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9NO7 | EM | 2.13 Å | F=1-210 |
| 4Y4O | X-ray | 2.3 Å | 1F/2F=1-210 |
| 8CVL | X-ray | 2.3 Å | 1F/2F=1-210 |
| 8FC6 | X-ray | 2.35 Å | 1F/2F=1-210 |
| 8VTW | X-ray | 2.35 Å | 1F/2F=1-210 |
| 4W2F | X-ray | 2.4 Å | BF/DF=1-210 |
| 6XHV | X-ray | 2.4 Å | 1F/2F=1-210 |
| 7RQA | X-ray | 2.4 Å | 1F/2F=1-210 |
| 7RQE | X-ray | 2.4 Å | 1F/2F=1-210 |
| 8CVJ | X-ray | 2.4 Å | 1F/2F=1-210 |
| 8VTU | X-ray | 2.4 Å | 1F/2F=1-210 |
| 8VTX | X-ray | 2.4 Å | 1F/2F=1-210 |
| 9MTP | X-ray | 2.4 Å | 1F/2F=1-210 |
| 10PX | X-ray | 2.45 Å | 1F/2F=1-210 |
| 7RQB | X-ray | 2.45 Å | 1F/2F=1-210 |
| 8FC4 | X-ray | 2.45 Å | 1F/2F=1-210 |
| 8G2A | X-ray | 2.45 Å | 1F/2F=1-210 |
| 9D0I | X-ray | 2.45 Å | 1F/2F=1-210 |
| 4Y4P | X-ray | 2.5 Å | 1F/2F=1-210 |
| 6XHW | X-ray | 2.5 Å | 1F/2F=1-210 |
Showing 20 of 270 experimental structures (best resolution first).
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