Sandbox Reserved 788

From Proteopedia

This is the of Listeria innocua Phosphofructokinase, with an associated ATP, several magnesium ions (green), and glycerol molecule. Phosphofructokinase is part of the glycolytic pathway. It adds a phosphate group from ATP to fructose 6-phosphate, to form fructose 1,6-bisphosphate. Phosphofructokinase contains 10 . The pattern of shows there to be a mixture of parallel and anti-parallel β-sheets. The parallel sheets can be identified by the angled hydrogen bonds, while the anti-parallel sheets contain straight hydrogen bonds. A display of the hydrophobic (orange) and hydrophilic (blue) shows that the hydrophobic groups are predominantly in the center of the protein, while the hydrophilic groups occupy the periphery and the active site. associate with the surface and active site of the enzyme. The position of the water molecules corresponds with the of the hydrophilic side chains, which is to be expected. The that the model displays interact with a molecule of glycerol (lavender), which is most likely an artifact of the purification and crystallization of the protein, the ATP (purple), and the magnesium ions(pink). The residues that interact with the glycerol are mostly charged, consisting of a lysine, an arginine, an aspartic acid and a histidine. There are also some nearby glycines, but these are most likely just nearby residues the program detected. Since glycerol is polar, it makes sense that hydrophilic residues associate with it. The molecule of ATP has 2 aspartic acids, a glutamic acid, and a lysine that interact with it. There are also a number of uncharged residues that surround the ATP. Proteopedia did not detect any residues within 4 Angstroms of the magnesium ions. The (green) consists of four side chains, an alanine, an aspartic acid, and two glycines. And just for fun, the space-filling model of phosphofructokinase with its associated waters can be seen (orange = hydrophobic, maroon = hydrophilic, blue = water).

Reverse transcriptase Native with highlighted catalytic residues: Native RNase H: Native with both domains highlighted: Inhibited with highlighted catalytic: Inhibited with tyrosine residues: Native tyrosine residues: Just inhibited: Native binding pocket: Native binding pocket spacefill: