Large ribosomal subunit protein bL25 (rplY) is a 237-residue protein from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9RX88.
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The mean pLDDT of this model is 80.1 (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 | 30% |
| 70 to 90 | Confident: backbone generally right | 50% |
| 50 to 70 | Low: treat with caution | 14% |
| Below 50 | Very low: often disordered regions | 6% |
What pLDDT means and how to read it
This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit. This protein has three domains. The N-terminal one is bound on the solvent face, the middle domain fills the space between the 5S rRNA and the L11 arm contacting the 23S rRNA while the C-terminal domain is on the edge of the intersubunit interface and contacts the A site. The protein conformation changes upon binding of a tRNA mimic to the A site, although the mimic does not interact directly with CTC itself, consistent with CTCs presumed role in moderating A site binding
Part of the 50S ribosomal subunit. Contacts proteins L11 and L16, the A site tRNA, and the 5S and 23S rRNAs
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5DM6 | X-ray | 2.9 Å | S=1-175 |
| 2ZJR | X-ray | 2.91 Å | S=1-237 |
| 5DM7 | X-ray | 3.0 Å | S=1-175 |
| 1NKW | X-ray | 3.1 Å | T=1-237 |
| 4IO9 | X-ray | 3.2 Å | S=1-237 |
| 4IOA | X-ray | 3.2 Å | S=1-237 |
| 7A0S | X-ray | 3.22 Å | S=1-175 |
| 3PIO | X-ray | 3.25 Å | S=1-237 |
| 1NWY | X-ray | 3.3 Å | T=1-237 |
| 2ZJQ | X-ray | 3.3 Å | S=1-237 |
| 3CF5 | X-ray | 3.3 Å | S=1-237 |
| 7A0R | X-ray | 3.3 Å | S=1-175 |
| 7A18 | X-ray | 3.4 Å | S=1-175 |
| 1SM1 | X-ray | 3.42 Å | T=1-237 |
| 5JVG | X-ray | 3.43 Å | S=1-237 |
| 3PIP | X-ray | 3.45 Å | S=1-237 |
| 1NJP | X-ray | 3.5 Å | T=1-237 |
| 1NWX | X-ray | 3.5 Å | T=1-237 |
| 1XBP | X-ray | 3.5 Å | T=1-237 |
| 3DLL | X-ray | 3.5 Å | S=1-237 |
Showing 20 of 33 experimental structures (best resolution first).
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