From Proteopedia
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Introduction
The in chain A of adenylate kinase shows multiple alpha helicies and beta sheets. These can be shown in different colors, with the alpha helicies shown in cyan and the beta sheets shown in red. The within the structure of the protein can also be displayed in green. These can be scene within the alpha helicies, helping maintain the structure of the helix, and are also between beta sheets. Most of the beta sheets are running parallel, as indicated by the crooked hydrogen bonds. They are crooked due to the position of the carbonyl oxygens and amide hydrogens in the structure. This formation is less stable than the straight, parallel hydrogen bonding of the antiparallel sheets. The on the structure can be seen in yellow sticks. Generally, these residues are clustered in the center of the protein due to the hydrophobic effect created by the surrounding water molecules. The are shown in purple here, and they are generally on the outside of the protein, shielding the hydrophobic residues. There are also around and inside the protein. Water helps stabilize the protein through the hydrophobic effect and also interacts/surrounds the binding site in the center of the protein. The is able to bind to the protein through the polar, charged parts of the active site that are shown in red and blue (red being anionic and blue being cationic). The are also shown in green. These residues specifically react with the substrate.
