Sandbox Reserved 1456: Difference between revisions
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The <scene name='79/799584/Ligand_ckc_2/2'>ligand</scene> of this molecule is (3S)-3,7-diaminoheptan-2-one, referred to as CKC. CKC has the same structure as lysine, having two protonated amine groups and a carboxylic acid group all capable of hydrogen bonding. The side chain of CKC contains four carbon groups which allows for a hydrophobic interaction, shown in gray, with an amine group in blue at the end, giving this molecule polarity. Per usual, the N terminus is colored blue and the C terminus is colored red. This molecule hydrogen bonds with the three amino acids of the catalytic triad to stabilize the structure of Kgp. The structure of the complex is maintained by hydrogen bond formation and a hydrophobic interaction with Trp513, thus decreasing entropy of the system and producing a favorable complex. | The <scene name='79/799584/Ligand_ckc_2/2'>ligand</scene> of this molecule is (3S)-3,7-diaminoheptan-2-one, referred to as CKC. CKC has the same structure as lysine, having two protonated amine groups and a carboxylic acid group all capable of hydrogen bonding. The side chain of CKC contains four carbon groups which allows for a hydrophobic interaction, shown in gray, with an amine group in blue at the end, giving this molecule polarity. Per usual, the N terminus is colored blue and the C terminus is colored red. This molecule hydrogen bonds with the three amino acids of the catalytic triad to stabilize the structure of Kgp. The structure of the complex is maintained by hydrogen bond formation and a hydrophobic interaction with Trp513, thus decreasing entropy of the system and producing a favorable complex. | ||
The <scene name='79/799584/Catalytic_triad/ | The <scene name='79/799584/Catalytic_triad/3'>catalytic triad</scene> of Kgp is made up of Cys477-His444-Asp388. The ligand, CKC, is shown in red and the three amino acids of the catalytic triad are colored by elements (CPK). His444 and Asp388 use acid base catalysis with a covalent intermediate formed with Cys477 to cleave the peptide bond. The histidine imidazolium group transfers a proton to the leaving alpha-amine group of the cleavage product, leaving part of the substrate bound covalently as a thioester to the catalytic Cys477. | ||
The mechanism of action of Kgp is largely determined by its <scene name='79/799584/Active_site_2/2'>active site</scene> The ligand, CKC, is shown as a spacefill model colored by element while the three amino acids of the catalytic triad are shown in red and the other amino acids that play an important role in the active site but are not part of the catalytic triad are shown as ball and stick models colored by element. By binding the ligand to the active site, Kgp is now capable of performing its virulytic activities. The temporary stability of the ligand by the amino acids in the active site allows Kgp to be specific in its activity and achieve optimal function. They aid in stability by hydrogen bonding to the ligand as well as decreasing entropy by hydrophobic interactions in the hydrophobic part of the ligand. | The mechanism of action of Kgp is largely determined by its <scene name='79/799584/Active_site_2/2'>active site</scene> The ligand, CKC, is shown as a spacefill model colored by element while the three amino acids of the catalytic triad are shown in red and the other amino acids that play an important role in the active site but are not part of the catalytic triad are shown as ball and stick models colored by element. By binding the ligand to the active site, Kgp is now capable of performing its virulytic activities. The temporary stability of the ligand by the amino acids in the active site allows Kgp to be specific in its activity and achieve optimal function. They aid in stability by hydrogen bonding to the ligand as well as decreasing entropy by hydrophobic interactions in the hydrophobic part of the ligand. | ||