Sandbox 39: Difference between revisions

ADK is a protein made up of 214 amino acids. The <scene name='Sandbox_39/Adenylate_kinase_main_chain2/1'>mainchain</scene> of adenylate kinase  can be seen here in purple with the ligand in the middle of the protein. The <scene name='Sandbox_39/Adenylate_kinase_beta_sheets2/1'>secondary structure</scene> contains 12 alpha helices (light blue) and 7 beta sheets (yellow). The <scene name='Sandbox_39/Adenylate_kinase_hbonds2/1'>backbone hydrogen bonds</scene> hold the protein together and give it shape. The <scene name='Sandbox_39/Adenylate_kinase_hydro_resid4/1'>hydrophobic residues</scene> are located towards the center of the protein, away from water. The <scene name='Sandbox_39/Adenylate_kinase_philic_resid2/1'>hydrophilic residues</scene> are located mainly on the surface or outside of the protein where they will have contact with water and other molecules. The <scene name='Sandbox_39/Adenylate_kinase_ligand/1'>ligand</scene> is located in the center of protein. The ligand has six <scene name='Sandbox_39/Adenylate_kinase_cat_residues/1'>catalytic residues</scene> that allow it to bind to ADK's target protein (catalytic residues shown in white within the green ligand). These catalytic residues are known as the active site. The <scene name='Sandbox_39/Adenylate_kinase_solv_w_lig/1'>ligand also has minimal water contact</scene> because it is located in the center of the protein (ligand is orange and water is displayed by space filling model). It is important to be shielded from water so that nothing interferes with the active site of the protein.