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Tutorial: Analysing an Active Site

In this example, we will look at the active site of the lactate dehydrogenase (pdb entry 1ldm).

Step by Step

  • First of all, open the pdb file 1LDM (it is included in the tutorial package).
  • Select the "Compute H-bonds" item of the "Tools" menu.
  • Click on the control panel window, scroll to the bottom (or hit the page down key), and select the groups "NAD1" and "OXM2". They should become red in the control panel. If they don't, it is a good idea to read the "Control Panel Selection" section).
  • Now, choose the item "Show Only H-bonds from selection" of the "Display Menu". Then choose the item "Show only groups with visible H-bond" of the same menu. Finally hit the "=" key of the numerical keypad (right mouse button for PC) to rescale and recenter the view.

If you wish to learn the basic manipulation of Swiss-PdbViewer through a tutorial, I recommend that you have a look at the one prepared by Prof. Gale Rhodes from the University of Southern Maine Portland. This tutorial has been prepared specifically for students and gives a lot of useful information not only on Swiss-PdbViewer manipulation, but also on general protein structure. As Prof. Gale Rhodes has spent a lot of time playing with the program, some interesting tips and details missing from my main documentation are unveiled.

You can also find a tutorial developed by Simon Andrews at this place

At this stage, you should be in this situation.

active site

  • Now you can measure distances using the tools located at the top of the display window, or show the H-bonds distances with the appropriate item of the "Display" menu.