Sandbox 47

Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. spinqualitylabelsall models Adenylate Kinase Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Introduction Adenylate kinase has homologs in many species and is an enzyme that converts one ATP and one AMP into two ADP molecules. For simplicity this page will focus on the form found in the bacterium Yersinia pestis. It usually functions with two identical subunits, Chain A and chain B, but for simplicity it is easier to focus on one chain. Structural Elements Adenylate kinase has multiple units of Secondary Structure, including alpha helices (blue) and beta sheets (red). The protein structure is held together with hydrogen bonds (green, not working). Looking at the hydrogen bonds demonstrates that the sheets are parallel in conformation, because the hydrogen bonds form trapezoids. The Hydrophobic Residues (gray) of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the polar residues (orange) are either on the exterior surface, where they can be accessed by the solvent, or in close interaction with each other. Some polar residues also center around the entrance to the active site, to aid the desolvation of the ligand. A combined view of both the Hydrophillic and Hydrophobic Residues allows one to see the general patterns of arrangement relative to each other. The hydrophillic residues often find themselves in interactions with the water (purple) that is solvating the enzyme. Water surrounds the outer surface of the protein, which is to be expected, but it is also possible to see that water molecules have interactions in some of the deeper parts of the protein as well, especially near the active site. Of course, the areas of the protein that interact with the substrates are the most interesting parts, so the ligand stabilizing residues (red) are important to note. The residues of the active site are the most critical parts of the protein, because they actually do the chemical reactions of the enzyme. The active site residues (purple) are shown here. Sources https://www.proteopedia.org/wiki/index.php/Adenylate_kinase Scenes (Just for reference) Chain A Secondary Structure hydrogen bonds Hydrophobic Residues Polar Residues Hydrophillic and Hydrophobic Residues Water ligand stabilizing residues active site