CRISPR system Cascade subunit CasD (casD) is a 224-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q46898.
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The mean pLDDT of this model is 90.8 (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 | 75% |
| 70 to 90 | Confident: backbone generally right | 17% |
| 50 to 70 | Low: treat with caution | 6% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA)
Part of the Cascade ribonucleoprotein complex, with stoichiometry CasA(1),CasB(2),CasC(6),CasD(1),CasE(1)-crRNA(1). Interacts directly with CasA and CasC. Stable subcomplexes of CasBCDE-crRNA and CasCDE-crRNA also form, both of which are able to bind target dsDNA, and at least CasCDE is able to form R-loops. CasCDE and CasCE complexes have endonuclease activity. Binding of target ssRNA or dsDNA…
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5H9F | X-ray | 2.45 Å | J=1-224 |
| 4U7U | X-ray | 3.0 Å | K/W=1-224 |
| 4QYZ | X-ray | 3.03 Å | J=1-224 |
| 5CD4 | X-ray | 3.2 Å | H/T=1-224 |
| 5H9E | X-ray | 3.21 Å | J=1-224 |
| 4TVX | X-ray | 3.24 Å | H/T=1-224 |
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