How to see conserved regions
Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see Introduction to Evolutionary Conservation.
Conservation in ProteopediaConservation in Proteopedia
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.
If the molecule of interest lacks the Evolutionary Conservation line below the molecule, please see the instructions below.
My Molecule Has No Evolutionary Conservation Line in ProteopediaMy Molecule Has No Evolutionary Conservation Line in Proteopedia
If, in Proteopedia, the molecule of interest lacks the Evolutionary Conservation line below the molecule:
- 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 ProteopediaConservation in Green Links in Proteopedia
You can show ConSurf-colored molecules with green links in Proteopedia.
Conservation in FirstGlanceConservation 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.
- Enter the PDB code in the search slot in Proteopedia.
- At the page title with the PDB code, click on [show] in the line labeled Evolutionary Conservation beneath the molecule. (If there is no such line, see below.)
- The Evolutionary Conservation section is now expanded. Click on the link Complete Results at ConSurfDB.
- At ConSurfDB, click on the button for the chain of interest under View 3D structure colored by conservation in FirstGlance in Jmol. (You can only see one chain at a time at ConSurfDB. Here is the reason.)