PyMOL Project
Create one powerpoint slide for the poster. The poster should contain at least three figures: one (1) highlighting the secondary structure and two (2) active site images. Each Figure must have a caption—for the active site images, be sure to describe the types of interactions you are showing in the image, and refer to any specific amino acid residues (involved in catalysis or inhibitor binding) by their amino acid number. The PDB is 2Z5X. I included an example of how the poster should look like for the PyMOL image part in the file.
Full instruction:
A. Go to the RCSB PDB and examine all ligands bound to the protein structure. One of these
will be your drug, but there may be others. List all of the ligands and their role (e.g.,
substrate, product, coenzyme, inhibitor, cofactor, ions unrelated to function etc.) Note that
the ligands are listed on the structure’s PDB entry page. Insert at least one PyMOL image
zoomed out to show your entire enzyme. Be sure that each of these molecules is clearly
visible in your snapshot; you might label these in PyMOL or in the program you create
your poster in.
Some ligands are not relevant to your enzyme’s biological function (i.e., are only there due
to crystallization conditions and/or are not located at a site in the enzyme where they give
information about the true substrates, products, cofactors, or regulators). You will need to
read the manuscript and potentially the experimental procedures to figure out a molecule’s
role in the structure.
B. Create at least two PyMOL snapshots zoomed in on just the active site of your enzyme.
List the catalytic residues (e.g., Ser261, His342). Clearly show these residues in your
snapshots. Highlight other molecules in the structure that are involved in the reaction
catalyzed by your enzyme (substrates, products, cofactors, coenzymes, etc.). You may
hide the bound drug/inhibitor to create this image.
C. Zoom in on the drug bound to your enzyme (note that it may be in the active site, or bound
to another part of the protein, depending on the type of inhibitor). Name the molecule that
you have chosen. Illustrate all noncovalent interactions between this molecule and the
enzyme using at least one PyMOL snapshot. Include hydrogen bonds, hydrophobic
packing, and salt bridges. Describe all of the polar interactions, referencing the specific
amino acid side chain that is involved in the interaction by its three-letter code and residue
number and describing how it contacts the drug. Also highlight one nonpolar interaction.Attached good examples
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