Large ribosomal subunit protein uL1 (rplA) is a 229-residue protein from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q5SLP7.
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The mean pLDDT of this model is 91.5 (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 | 71% |
| 70 to 90 | Confident: backbone generally right | 29% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Directly binds to 23S rRNA. Forms what is known as the L1 stalk, which protrudes beyond the 70S ribosome surface. The stalk is preferentially stabilized in 70S versus 50S crystals. Interacts with the E site tRNA, blocking the exit path. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA
Part of the 50S ribosomal subunit. In 70S ribosomes plus EF-P, the L1 stalk moves significantly, while uL1 shifts to a position in the E-site, contacting EF-P (PubMed:19696344)
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3TG8 | X-ray | 1.95 Å | A=1-229 |
| 5NPM | X-ray | 2.7 Å | A=10-229 |
| 4V51 | X-ray | 2.8 Å | BC/DC=1-229 |
| 4WPO | X-ray | 2.8 Å | AC/CC=2-229 |
| 4WQF | X-ray | 2.8 Å | AC/CC=2-229 |
| 4WQU | X-ray | 2.8 Å | AC/CC=2-229 |
| 4WQY | X-ray | 2.8 Å | AC/CC=2-229 |
| 4V9H | X-ray | 2.86 Å | BC=1-229 |
| 4V90 | X-ray | 2.95 Å | BC=2-229 |
| 5E81 | X-ray | 2.95 Å | 71/79=1-229 |
| 4V7L | X-ray | 3.0 Å | BC/DC=1-229 |
| 5HAU | X-ray | 3.0 Å | 1C/2C=1-229 |
| 4WF1 | X-ray | 3.09 Å | B5=19-225 |
| 4V5J | X-ray | 3.1 Å | BC/DC=1-229 |
| 4V5L | X-ray | 3.1 Å | BC=1-229 |
| 4V5P | X-ray | 3.1 Å | BC/DC=1-229 |
| 4V5Q | X-ray | 3.1 Å | BC/DC=1-229 |
| 4V5R | X-ray | 3.1 Å | BC/DC=1-229 |
| 4V5S | X-ray | 3.1 Å | BC/DC=1-229 |
| 4V6A | X-ray | 3.1 Å | BC/DC=1-229 |
Showing 20 of 68 experimental structures (best resolution first).
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