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PDB: 2PX6
The assignment should contain at least three figures: one (1) highligh
PDB: 2PX6
The assignment 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. I included an example on the file for how the assignment should look like. The three images need to be created using PyMOL for PDB: 2PX6 and using the white background.
Active site and enzyme-drug interactions
A. Include an image of the chemical structure of your drug molecule.
B. Create at least two PyMOL figures zoomed in on just the active site of your
enzyme. List the catalytic residues (e.g., Ser261, His342). Clearly show these
residues. 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, or use a secondary, unbound structure 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 inhibitor type). Illustrate all
noncovalent interactions with measurements between this molecule and the
enzyme using at least one PyMOL figure. Include all hydrogen bonds and salt
bridges, clearly distinguishing these types of interactions. Also, show one nonpolar
interaction (3.3-4.0 Angstrom range).
D. Describe all of the interactions, referencing the specific amino acid side chain that is
involved in the interaction by its three-letter code and residue number and describing
the type of interaction with the drug. To save space, you may group them by type of
interaction.
VII. Figure Captions
For each figure, include a caption or description that helps the viewer understand
what they are seeing. A good figure caption briefly describes:
1. The figure content
2. Any coloring/labeling schemes to help the viewer interpret the image.
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