Sandbox 50: Difference between revisions

The active site, like mentioned above, is where the substrates binds to the enzyme to be catalyzed. In ADK, the <scene name='Sandbox_50/Ak_ligand_contact1/1'>ligand_contacts</scene> (gray, blue, pink), is in the interior of the protein. The pink is where the ligand binds directly. In the active site there are hydrophobic residues present, which allows for hydrophobic interactions between the enzyme and the ligand. Hydrogen bonds forming between the enzyme and the substrates. This helps stabilizes the substrate in the site, so that it can be catalyzed. There are also six <scene name='Sandbox_50/Ak_catalytic_residues1/1'>catalytic_residues</scene>, which are specifically involved in the catalyzes of the substrates, which are highlighted black on the image. The catalytic residues are all charged residues and include Lysine, Aspartic acid, and Arginine. These residues allow for electrostatic interactions but can be effected by the presence of the water in the active site.

The <scene name='Sandbox_50/Ak_water6/1'>solvent</scene>, which is water (blue), can be co-crystallized with the enzyme. The water can be found all around the protein but there is also some water molecules in the active site, around the ligand. This further indicates why the hydrophilic residues are found on the surface, and the nonpolar residues are buried away. The water creates a hydrophilic environment, and the hydrophobic residues aggregate together in the interior, which is the hydrophobic effect and drives the water out. So for the most part, there are not water molecules in between the secondary structure, but there are some water molecules in the open spaces between the backbone.The hydrophilic residues in the active site cause water to be present there, and also make it easier for the ligand to enter and facilitates in the reaction.