Go to the Protein Data Bank web site http://www.rcsb.org/pdb

Locate the blue column on the left of the page and find the button for the tutorial. Take the tutorial.

1. Go back to the Protein Data Bank home page and search for 4PFK.

2. Go down to Chemical Component and locate the ligands. You can view their structures by clicking on the View link or check the structures below. Click View under Ligand Interactions for one of the ligands. This will download and open Ligand Explorer for PFK.

3. Locate the ball and stick molecules (the ligands). You should be able to find three: one fructose-6-phosphate, and two ADP's, each with an associated Mg ion (green ball). One ADP is close to the fructose-6-phosphate, and the other is not. Hydrogens are not shown in these structures, which means that a water molecule will look like a red ball.

4. On the menu on the left choose F6P (fructose-6-phosphate) in Step 1.
Choose hydrophilic interactions in Step 2. Click Apply at the bottom.
With what amino acid side chains is F6P interacting?
Record the one-letter abbreviation and number of the residue(s).
You may need to select part of the molecule and rotate the diagram in order to locate the name and number of the residue. You can click the Reset button in order to return to the original orientation.
If necessary, use the sequence at the top of the diagram to identify the amino acids; each highlighted (shaded) letter indicates an amino acid with an interaction with the ligand. If you click on one of the letters, the side chain will disappear. You can add the side chain back by clicking again.

Repeat for hydrophobic interactions and then for bridged H-bonds. Each time you change the type of interaction click "Apply" in order to see the interaction.

What type of interaction is most important for positioning F6P? That is, for which type of interaction do you see the most lines?

5. Find an amino acid residue that is involved in both hydrophilic and hydrophobic interactions. Draw the structure of that amino acid and locate the parts involved in each type of interaction. Are they the same?

6. If you have time and are interested, click "Other" and Apply. Based upon the lines and the atoms connected, what type(s) of interaction does "Other" include?

Repeat this process with the protein 1HMR.

7. Go down to Chemical Component and click View under Ligand Interactions for 9-octadecenoic acid (ELA). This will download and open Ligand Explorer.

8. Locate the ball and stick molecule (the ligand).

9. On the menu on the left choose ELA (9-octadecenoic acid) in Step 1.
Choose hydrophilic interactions in Step 2. Click Apply at the bottom.
With what amino acid side chains is ELA interacting?
Record the one-letter abbreviation and number of the residue(s).
Repeat for hydrophobic interactions and then for bridged H-bonds. Each time you change the type of interaction click "Apply" in order to see the interaction.

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