Sandbox 32
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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.
Adenylate Kinase (PDB ID #: 1ake)The A Chain by itself may be in a slightly different conformation than when it is attached to the B chain (as found in nature). Adenylate Kinase contains both types of secondary structure, alpha helices and beta sheets. In this scene, alpha helices are in light blue and beta sheets are in yellow. The hydrogen bonding highlighted in this scene shows us that the secondary structure (helices and sheets) is held together by hydrogen bonds. The beta sheets appear to be parallel, as the H-bonds are not all aligned in one direction. Hydrophobic side chains, highlighted here in pink, tend to point towards the inside of the molecule where they do not have to interact with the polar water molecules. The hydrophilic side chains, highlighted here in blue along with the transparent pink hydrophobic residues, tend to be pointed towards the outside of the protein, where it will interact with the cytosol. Water molecules (shown in blue) surround and solvate the protein. The ligand is highlighted in green. The waters seem to congregated on one side than the other, possibly to make room for chain B to bind. Sidechain and ligand interactions are shown in this scene. The ligand is in orange, and the interacting side chains are in dark blue and red. Of these contacting residues, only some actually catalyze the reaction on the substrate. These active site residues are highlighted in red. These are the residues which interact chemically with the substrate to turn it into product. The non-active site residues are important in substrate (or ligand) binding. |
