Sonic hedgehog protein (SHH) is a 462-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q15465.
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The mean pLDDT of this model is 78.4 (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 | 47% |
| 70 to 90 | Confident: backbone generally right | 27% |
| 50 to 70 | Low: treat with caution | 10% |
| Below 50 | Very low: often disordered regions | 17% |
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:29954986, PubMed:29995851, PubMed:30139912, PubMed:31127104, PubMed:31548691). 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 (By similarity). Both autoproteolysis and a cholesterol transferase activities occur in the…
Interacts with HHATL/GUP1 which negatively regulates HHAT-mediated palmitoylation of the SHH N-terminus (By similarity). Interacts with HHIP (PubMed:19561609). Interacts with glypican GPC3 (By similarity)
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 |
|---|---|---|---|
| 6PJV | X-ray | 1.43 Å | A=29-197 |
| 8Z3A | X-ray | 1.75 Å | A=29-197 |
| 8Z39 | X-ray | 1.8 Å | A=29-197 |
| 3MXW | X-ray | 1.83 Å | A=29-197 |
| 3M1N | X-ray | 1.85 Å | A/B=23-197 |
| 8Z2V | X-ray | 1.89 Å | A=29-197 |
| 8YYZ | X-ray | 1.9 Å | A=29-197 |
| 7URF | EM | 2.8 Å | B=24-30 |
| 3HO5 | X-ray | 3.01 Å | H=29-197 |
| 7MHZ | EM | 3.2 Å | B=24-31 |
| 6RMG | EM | 3.4 Å | B=21-197 |
| 6E1H | EM | 3.5 Å | C=24-197 |
| 6RVD | EM | 3.5 Å | C=24-197 |
| 7RHQ | EM | 3.53 Å | C=24-197 |
| 6DMY | EM | 3.6 Å | B=24-197 |
| 6N7H | EM | 3.6 Å | C=24-197 |
| 6OEV | EM | 3.8 Å | C=23-197 |
| 7E2I | EM | 4.07 Å | G=1-462 |
| 6N7K | EM | 6.5 Å | C/F=24-197 |
| 6N7G | EM | 6.8 Å | C/F=24-197 |
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