Sandbox 37: Difference between revisions

Papain's three-dimensional structure is at 1.65 Angstrom resolution. It consists of one polypepetide chain that is made up of 212 amino acids residues. There are three <scene name='Sandbox_37/Papain_disulfide_bonds/1'>disulfide bonds</scene> present in the enzyme that maintains the protein's structure. Papain consists of 25% alpha helices and 21% beta sheets within its <scene name='Sandbox_37/Papain_beta-alpha/1'>secondary structure</scene>. Alpha helices are shown in red and beta sheets are shown in green. The enzyme's structure has a mixture of <scene name='Sandbox_37/Papain_hydrophobic/7'>hydrophobic residues</scene> shown in yellow and hydrophilic residues shown in purple. This corresponds to the protein's <scene name='Sandbox_37/Papain_polar/1'>polar residues</scene> shown in orange and nonpolar residues shown in green. Papain is naturally found with many <scene name='Sandbox_37/Ligand/3'>ligands</scene>. The majority are methanol molecules because the crystallization medium is 62% (w/w) methanol in water and only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules.<ref>http://www.pdb.org/pdb/explore.do?structureId=9PAP</ref> Here, the enzyme's sulfhydryl group can also be seen which is necessary for the activity of the enzyme. <scene name='Sandbox_37/Papain_van_der_waals/1'>Van der Waals interactions</scene> and <scene name='Sandbox_37/Papain_hydrogen_bonds/1'>hydrogen bonds</scene> between the ligands and protein maintain the structural domains of papain. Water molecules are depicted as pink spheres.