Sandbox 50: Difference between revisions

The active site, like mentioned above, is where the ligand/substrate 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. There are six <scene name='Sandbox_50/Ak_catalytic_residues1/1'>catalytic_residues</scene>, which are specifically involved in the catalyzes of the substrates forming hydrogen bonds with the ligand, and they are highlighted black on the image. They are all charged residues and include Lysine, Aspartic acid, and Arginine. The other residues also interact with the ligand, but only with weak electrostatic and hydrophobic interactions because they are further away.  

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 drives the hydrophobic effect, burying the hydrophobic residues in the interior. The hydrophilic residues in the active site cause water to be present there, and also make it easier for the ligand to enter. For the most part, there are not water molecules in between the secondary structure because that is where the hydrophobic residues reside, but there are some water molecules in the open spaces of the backbone.