Sandbox Reserved 788
From Proteopedia
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<Structure load='3IE7' size='500' frame='true' align='right' caption='Phosphofructokinase' scene='Insert optional scene name here' /> | <Structure load='3IE7' size='500' frame='true' align='right' caption='Phosphofructokinase' scene='Insert optional scene name here' /> | ||
| - | This is the <scene name='56/563200/Phosphofructokinase/1'>secondary structure</scene> of ''Listeria innocua'' Phosphofructokinase, with an associated ATP, several magnesium ions, and glycerol molecule. | + | This is the <scene name='56/563200/Phosphofructokinase/1'>secondary structure</scene> of ''Listeria innocua'' Phosphofructokinase, with an associated ATP, several magnesium ions, 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. |
| - | It contains 10 <scene name='56/563200/Highlighted_alpha_and_beta/3'>α-helices and 14 β-sheets</scene>. The pattern of <scene name='56/563200/H-bonds/2'>backbone hydrogen bonding</scene> 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) <scene name='56/563200/Hydrophobic_and_hydrophilic/4'>side chains</scene> shows that the hydrophobic groups are predominantly in the center of the protein, while the hydrophilic groups occupy the periphery and the active site. <scene name='56/563200/Water_localization/2'>Water molecules</scene> associate with the surface and active site of the enzyme. The position of the water molecules corresponds with the <scene name='56/563200/Side_chain_sticks_with_water/1'>locations</scene> of the hydrophilic side chains, which is to be expected. The <scene name='56/563200/Ligand_binding/ | + | Phosphofructokinase contains 10 <scene name='56/563200/Highlighted_alpha_and_beta/3'>α-helices (green) and 14 β-sheets (blue)</scene>. The pattern of <scene name='56/563200/H-bonds/2'>backbone hydrogen bonding</scene> 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) <scene name='56/563200/Hydrophobic_and_hydrophilic/4'>side chains</scene> shows that the hydrophobic groups are predominantly in the center of the protein, while the hydrophilic groups occupy the periphery and the active site. <scene name='56/563200/Water_localization/2'>Water molecules (light blue)</scene> associate with the surface and active site of the enzyme. The position of the water molecules corresponds with the <scene name='56/563200/Side_chain_sticks_with_water/1'>locations</scene> of the hydrophilic side chains, which is to be expected. The <scene name='56/563200/Ligand_binding/5'>ligand interacting residures</scene> 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, and the ATP (purple)and 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 <scene name='56/563200/Active_site/4'>active site</scene> (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 <scene name='56/563200/Spacefilling/1'>here</scene> (orange = hydrophobic, maroon = hydrophilic, blue = water). |
Revision as of 18:39, 15 October 2013
| This Sandbox is Reserved from Oct 10, 2013, through May 20, 2014 for use in the course "CHEM 410 Biochemistry 1 and 2" taught by Hanna Tims at the Messiah College. This reservation includes Sandbox Reserved 780 through Sandbox Reserved 807. |
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This is the of Listeria innocua Phosphofructokinase, with an associated ATP, several magnesium ions, 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, and the ATP (purple)and 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).
