Please answer the following questions using PyMOL (https://pymol.org/2/). You should be able to use the trial license to do this assignment. Submit via email a single file in PDF format Ensure that all images are labeled and embedded in this document. In this exercise you will find a PDB file from the protein data bank (https://www.rcsb.org/) and interrogate its structure using PyMOL. Make sure this file has a small molecule ligand of reasonable size (at least 10 heavy atoms; when in doubt try to find a protein with a ligand that obeys Lipinski's rule of 5: https://en.wikipedia.org/wiki/Lipinski%27s_rule_of_five ). Also, make sure this is a crystal structure (not an NMR or cryo-EM structure). If you have no idea where to start, try this website: https://pdb101.rcsb.org/browse. When making your images, do not use screen captures. Instead use the Save Image As option under the File menu and insert the image into your PDF. 1. Find an appropriate protein for this assignment. Provide the PDB code, date of submission, name, and function of the protein you selected? Your protein must meet the following criteria: a. Electron density file submitted b. A small molecule ligand (NOT a small molecule that is part of the crystallant or buffer, i.e. it should be either a known ligand or a drug-like compound whose interactions the structure was aiming to explore) c. At least two protein chains 2. How many residues are present? How many chains? How many crystallographic waters? How many ligands? Attach a picture of your protein with the protein colored by chain in surface representation, and any ligands colored by atom type in spheres representation. 3. Which stretch of amino acids (other than the N and C termini) is most flexible and can you hypothesize any biological significance for this flexibility? Attach a picture of a putty diagram colored by b-factor that supports your answer. 4. What sort of interactions appear to be stabilizing the ligand in the active site? Are there water molecules in the active site (and if so, how many)? Does the electron density well support the orientation of the ligand that is observed in the model? Attach a picture of your protein showing the electron density around the ligand at 1.0 sigma and all hydrogen bonds between the ligand and the protein (you will need to change the color of the isomesh and the h-bonds to do this on a white background, also make sure you use the carve option with isomesh). Show residues within 5 angstroms of the ligand as sticks and be sure to distinguish the ligand from the protein (either using coloring or different representations). 5. If you wanted to attach a hexa-his tag to this protein, which terminus is likely to be a better candidate (assuming the protein crystallizes the same way, which tag is least likely to upset crystal packing)? Use the symexp command to investigate this. Try to use the build tools and the mutagenesis wizard to fit a hexa-his tag on one of the termini. Attach an image showing how it fits between crystal contacts. (Do your best here, it doesn't have to be directly attached to the protein, just show how it could fit). 6. Use the fancy representations described in http://www.pymolwiki.org/index.php/Gallery as a guide to create a stylish picture of your protein. You will get full credit for doing something fancy like in the examples (this involves changing the rendering settings).