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To appreciate the structural features and complexity of proteins, it’s best to view them in 3D and manipulate the structures yourself. Using PyMol, you can explore the different structural features you’ve learned about, for every protein you could think of. Follow the instructions shown in bold blue. Use the PDB Loader Service to load up ubiquitin (1ubq). Plugin > PDB Loader Service To find out about ubiquitin, look it up on the PDBE website. (http://www.pdbe.org) Hide everything as shown in the screen shot. H > Everything You can choose to show the protein as lines, sticks or ribbons (make sure to ‘Hide everything’ before you change between views). Choose to show the protein as a cartoon. S > Cartoon Next, click the ‘S’ at the bottom of the screen. This will allow you to see the sequence of amino acid residues which make up the primary structure of your chosen protein. This gives you a good idea of the secondary structural features (α-helices, β-sheets) in the protein and makes it easier to manipulate. The amino acid sequence is shown at the top of the screen using their one-letter codes. You can use your mouse to highlight particular amino acid residues to see where they are in the protein. Alternatively, you can colour the protein by secondary structural feature (C > by ss) as shown below. α helices, β sheets and loops are shown in different colours. You can also see which amino acid residues make up which part of the protein. To see the individual amino acid residues and their R-groups, choose to display the side chains. S > side chain > lines To view the hydrogen bonds responsible for keeping the secondary structures in place, display the polar contacts. Explore some more features of PyMol until you feel comfortable with how it works and the features that are available to help you understand and visualise protein structure. A > find > polar contacts > just intramain chain Produced by Lucy Jakubecz at Newcastle University as part of an MChem project.