Small nuclear ribonucleoprotein Sm D2 (SNRPD2) is a 118-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P62316.
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The mean pLDDT of this model is 90.6 (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 | 78% |
| 70 to 90 | Confident: backbone generally right | 16% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28076346, PubMed:28502770, PubMed:28781166, PubMed:32494006). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28076346, PubMed:28502770, PubMed:28781166). As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs (PubMed:15146077)
Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28076346, PubMed:28502770, PubMed:28781166, PubMed:32494006, PubMed:36797247). Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2,…
Cytoplasm, cytosol, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4F7U | X-ray | 1.9 Å | B/D=1-118 |
| 1B34 | X-ray | 2.5 Å | B=1-118 |
| 5XJL | X-ray | 2.5 Å | B=1-118 |
| 7EVO | EM | 2.5 Å | a=1-118 |
| 5XJU | X-ray | 2.58 Å | B=1-118 |
| 8H6L | EM | 2.6 Å | 2c/4c/5c=1-118 |
| 8H6K | EM | 2.7 Å | 2c/4c/5c=1-118 |
| 8HK1 | EM | 2.7 Å | a=1-118 |
| 8C6J | EM | 2.8 Å | a/m=1-118 |
| 6ID1 | EM | 2.86 Å | d/k=1-118 |
| 7DVQ | EM | 2.89 Å | d/k=1-118 |
| 6ID0 | EM | 2.9 Å | d/k=1-118 |
| 5XJT | X-ray | 2.92 Å | B=1-118 |
| 6QW6 | EM | 2.92 Å | 42/52=1-118 |
| 6ICZ | EM | 3.0 Å | d/k=1-118 |
| 7VPX | EM | 3.0 Å | a/i=1-118 |
| 8I0R | EM | 3.0 Å | c/h=1-118 |
| 8I0T | EM | 3.0 Å | c/h=1-118 |
| 8I0V | EM | 3.0 Å | c/h=1-118 |
| 9GCL | EM | 3.0 Å | i=1-118 |
Showing 20 of 80 experimental structures (best resolution first).
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