How to see conserved regions
From Proteopedia
Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see Introduction to Evolutionary Conservation.
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Conservation in Proteopedia
Right click here to open a duplicate of this page in a separate tab or window so you can keep this page visible.
Enter your PDB code in the upper search slot at the left side of the either tab/window. This should take you to a page titled with your PDB code, such as 2hhd.
- Click the orange load full button to load all atoms in the model (rather than the initial simplified model, which loads only alpha carbon atoms).
- Look for the section Evolutionary Conservation and check a checkbox there to color the molecule according to ConSurfDB.
Not all pages titled with a PDB code have an Evolutionary Conservation section (example: 4d7b). If your does not, please see the instructions below.
My Molecule Has No Evolutionary Conservation Section in Proteopedia
If, in Proteopedia, the molecule of interest has no Evolutionary Conservation Section:
- Try looking directly in ConSurfDB. If it has no results for your molecule, or if you wish to obtain better results, try the next step.
- Calculate the conservation pattern yourself at the ConSurf Server. Here are instructions. When you get the result, there will be a link for showing that result in FirstGlance in Jmol.
Conservation in Green Links in Proteopedia
You can show ConSurf-colored molecules with green links in Proteopedia.
Conservation in FirstGlance
You might wish to explore a conservation-colored molecule in FirstGlance so you can hide portions of it, locate sequence numbers of interest, or examine the conservation of the amino acids that bind a ligand, or for other reasons. (Examples)
- Enter your PDB code at the ConSurf Database (ConSurfDB). In some cases, once you choose a single protein chain, there will be a link to view a pre-calculated evolutionary conservation pattern in FirstGlance.
- If not, you will need to calculate the evolutionary conservation pattern following these instructions.
You can only color one chain at a time by evolutionary conservation when using FirstGlance. Here is the reason.