Sonic hedgehog protein (Shh) is a 437-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q62226.
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The mean pLDDT of this model is 83.4 (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 | 55% |
| 70 to 90 | Confident: backbone generally right | 27% |
| 50 to 70 | Low: treat with caution | 10% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Precursor of sonic hedgehog, a morphogen that activates the smoothened signaling pathway, and which is essential for a variety of patterning events during development (PubMed:11389830, PubMed:31657721, PubMed:7736596, PubMed:7891723, PubMed:8824192). The C-terminal part of the precursor displays an autoproteolysis and a cholesterol transferase activity, resulting (1) in the cleavage of the full-length protein into two parts, Sonic hedgehog protein N-product and C-product (ShhN and ShhC, respectively) and (2) covalent attachment of a cholesterol moiety to the C-terminus of the newly generated ShhN (PubMed:7736596, PubMed:7891723, PubMed:8824192). Both autoproteolysis and a cholesterol…
Interacts with HHATL/GUP1 which negatively regulates HHAT-mediated palmitoylation of the SHH N-terminus (PubMed:18081866). Interacts with HHIP (PubMed:19561611). Interacts with glypican GPC3 (PubMed:18477453)
Endoplasmic reticulum membrane, Golgi apparatus membrane, Secreted, Cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1VHH | X-ray | 1.7 Å | A=34-195 |
| 3D1M | X-ray | 1.7 Å | A/B=26-189 |
| 4C4M | X-ray | 1.74 Å | A=40-195 |
| 3N1R | X-ray | 2.13 Å | A=40-195 |
| 4C4N | X-ray | 2.36 Å | A/B=40-195 |
| 7RPK | EM | 2.7 Å | H=26-189 |
| 2WG4 | X-ray | 3.15 Å | A=40-194 |
| 2WFX | X-ray | 3.2 Å | A=40-191 |
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