1) Go to Protein Data Bank. Enter in the term isocitrate dehydrogenase. For most of these questions, you must use either a PC and IE, or a Mac and Netscape 4.7x. Either way, you will need the free plugin called chime. If your computer is chime-ready, then you will see a small DNA molecule here:
2) Find the entry called 1AI3. Click on the small eye icon to the right of the PDB ID number.
3) From this new page, click on "Quick PDB". This does not require chime.
4) In the QuickPDB window, click on any part of the protein and find the amino acid you selected in the upper frame. Now click on the upper pull down menu that says "secondary structure" to highlight the protein's structure. What type of structure was your amino acid in? (red = alpha helix; yellow = beta strand; blue = no secondary structure)
5) Close the QuickPDB window. Now click on the "First Glance" link that does require chime. Click on the "off" button to stop the spinning. Click on the zoom button to zoom in. Click on the cartoon button and then the 2° structure button. Now toggle the ligands on and off. Can you identify the substrate isocitrate, the coenzyme NADP+ and the cofactor Mg2+?
6) Finally, click on the link that says "VRML (default options)". In a few seconds, you will see yet another way to render IDH. Use the option key and your mouse to zoom in and out. Can you see the three ligands now? Which way do you like best? Explain your answer.
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