Sandbox reserved 392: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Arthur Cox, Alyssa Graham, Jaime Prilusky

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 *The <scene name='Sandbox_reserved_392/Ligands/1'>ligands</scene> displayed in the molecule to the right are Coenzyme A, Tobramycin and 3'-Phosphate-Adenosine-5'-Diphosphate. <scene name='Sandbox_reserved_392/Coa/1'>Coenzyme A</scene> (CoA) is a coenzyme that synthesizes and oxidizes fatty acids. <scene name='Sandbox_reserved_392/Pap/1'>PAP's</scene> IUPAC name is [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methylphosphono hydrogen phosphate. The Protein in this molecule is represented as a <scene name='Sandbox_reserved_392/Protein_as_a_dimer/1'>dimer</scene>. A dimer is a chemical structure formed from two subunits. In the molecule to the left you can see the representation of this.
-*This structure focuses on the <scene name='Sandbox_reserved_392/Protein-ligand/1'>protein bond to the ligand</scene>. The red molecules represent an anionic or negatively charged interaction. The dark blue molecules emphasize the cationic or positively charged interactions. The cationic and anionic interactions are contributed to arginine, aspartic acid, or glycine amino acids. The light blue molecules represent histidine, which is a basic amino acid.
+*This structure focuses on the <scene name='Sandbox_reserved_392/Ligand_bound_to_protein/1'>protein bound to the ligand CoA</scene>. The red molecules represent an anionic or negatively charged interaction. The dark blue molecules emphasize the cationic or positively charged interactions. The cationic and anionic interactions are contributed to arginine, aspartic acid, or glycine amino acids. The light blue molecules represent histidine, which is a basic amino acid.
 * scene name='Sandbox_reserved_392/Hydrogen_bonds/2'>Hydrogen Bonds</scene> are attractive interactions (dipole-dipole) between an electronegative atom and hydrogen. The hydrogen bonds in this picture are displayed as yellow dashed lines.  This bond always involves a hydrogen atom. A hydrogen bond is stronger then a van-der-waals interaction but weaker then an ionic or covalent bond. The hydrogen bonds in this display are between the alpha helices and beta sheets. An ionic bond is an attraction between two molecules of opposite charge. Covalent bonds, the strongest type of bond, involves the sharing of electrons between two molecules.