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Solution 1: Retrieving IRAK2 3D structure using AlphaFold DB

Go to AlphaFold DB and type IRAK2 in the search box. The output page lists the IRAK2 predicted structure for different organisms. In this case, we want to select Homo sapiens (Figure 16):

Image displays the first AlphaFold DB output for the search "IRAK2". The displayed output is the prediction for the Homo Sapiens protein, and it includes the pLDDT score (67.76).
Figure 16 Results for “IRAK2” search in AlphaFold DB.

The protein page (Figure 17) provides various information, including the protein AlphaFold ID (in this case AF-O43187-F1-v4), the availability of experimental structures, and predictions for possible amino acids substitutions pathogenicity (AlphaMissense). The 3D structure can also be downloaded.

Image displays IRAK2 protein page in AlphaFold database. This include AlphaFold DB protein ID, a set of protein information (protein, gene, organism, Uniprot I, link to experimental structure, protein function) and representation of predicted structure and predicted aligned error.
Figure 17 IRAK2 page in AlphaFold DB.

Model evaluation

For easy visualisation, each domain in the predicted structure is colour-coded according to the Predicted Local Distance Difference Test Score (pLDDT), with a scale from orange/red (low confidence) to blue (high confidence). The numeric score is visible when placing the cursor over the domain of interest. AlphaFold DB also provides an average pLDDT, displayed in the protein overview. In the case of IRAK2, the average pLDDT is 67.76 (as for February 2025), which places the prediction in the low confidence range. In this case, it can be interesting to proceed with an independent method and then compare the results: you’ll try it yourself in the next page (Solution 2).