V(D)J recombination-activating protein 2 (Rag2) is a 527-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P21784.
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The mean pLDDT of this model is 76.3 (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 | 56% |
| 70 to 90 | Confident: backbone generally right | 8% |
| 50 to 70 | Low: treat with caution | 13% |
| Below 50 | Very low: often disordered regions | 23% |
What pLDDT means and how to read it
Core component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. DNA cleavage by the RAG complex occurs in 2 steps: a first nick is introduced in the top strand immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends and 2 blunt,…
Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2V89 | X-ray | 1.1 Å | A/B=414-487 |
| 2V87 | X-ray | 1.8 Å | A/B=414-487 |
| 2V85 | X-ray | 2.0 Å | A/B=414-487 |
| 2V88 | X-ray | 2.0 Å | A/B=414-487 |
| 2V86 | X-ray | 2.05 Å | A/B=414-487 |
| 2V83 | X-ray | 2.4 Å | A/B/C=414-487 |
| 6XNX | EM | 2.7 Å | B/D=3-361 |
| 5ZE0 | X-ray | 2.75 Å | B/D=1-387 |
| 5ZDZ | X-ray | 2.8 Å | B/D=1-387 |
| 6XNY | EM | 2.9 Å | B/D=3-361 |
| 9JPX | EM | 2.95 Å | B/D=1-527 |
| 5ZE1 | X-ray | 3.0 Å | B/D=1-387 |
| 9JQN | EM | 3.03 Å | B/D=1-527 |
| 6OES | EM | 3.06 Å | B/D=1-527 |
| 6CIK | X-ray | 3.15 Å | B/D=1-359 |
| 6CG0 | EM | 3.17 Å | B/D=1-520 |
| 4WWX | X-ray | 3.2 Å | X/Y=2-350 |
| 9JPU | EM | 3.25 Å | B/D/E=1-527 |
| 6OER | EM | 3.29 Å | B/D=1-527 |
| 5ZE2 | X-ray | 3.3 Å | B/D=1-387 |
Showing 20 of 34 experimental structures (best resolution first).
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