AFDB: Analyze the prediction for USP7

In this exercise, we will take a look at the interactive tool in the AlphaFoldDB.

1. Find the right entry in the AlphaFoldDB for protein USP7 (human).

2. Have a look at the PAE plot first. Can you identify how many different structural domains can be distinguished?

3. Which of these domains might interact with each other in the prediction?

4. Now, select a domain by drawing a rectangle on the PAE plot. What happens to the displayed structure?

5.  Based on the PAE plot, select two or more domains for which the relative position is predicted with high confidence. Do these domains interact?

In the image below, you have an overview of all individual domains and where they can be found on the PAE plot. (source: https://www.embopress.org/doi/10.15252/embr.202154046)