Sandbox Reserved 788 - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=Sandbox_Reserved_788 Sandbox Reserved 788 - Revision history 2026-04-11T09:37:53Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1907533&oldid=prev Student at 18:41, 29 March 2014 2014-03-29T18:41:27Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:41, 29 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 16:</td> <td colspan="2" class="diff-lineno">Line 16:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Just inhibited:<scene name='56/563200/Just_rvp/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Just inhibited:<scene name='56/563200/Just_rvp/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native binding pocket:<scene name='56/563200/Native_binding_pocket/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native binding pocket:<scene name='56/563200/Native_binding_pocket/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Native binding pocket spacefill:<scene name='56/563200/Native_binding_pocketspacefill/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1907532&oldid=prev Student at 18:38, 29 March 2014 2014-03-29T18:38:20Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:38, 29 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native tyrosine residues:<scene name='56/563200/Rt_with_y_residues/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native tyrosine residues:<scene name='56/563200/Rt_with_y_residues/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Just inhibited:<scene name='56/563200/Just_rvp/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Just inhibited:<scene name='56/563200/Just_rvp/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Native binding pocket:<scene name='56/563200/Native_binding_pocket/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1907531&oldid=prev Student at 16:01, 29 March 2014 2014-03-29T16:01:30Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 16:01, 29 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Inhibited with tyrosine residues:<scene name='56/563200/Rt_inhibited_with_y_residues/2'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Inhibited with tyrosine residues:<scene name='56/563200/Rt_inhibited_with_y_residues/2'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native tyrosine residues:<scene name='56/563200/Rt_with_y_residues/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native tyrosine residues:<scene name='56/563200/Rt_with_y_residues/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Just inhibited:<scene name='56/563200/Just_rvp/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1907510&oldid=prev Student at 20:22, 28 March 2014 2014-03-28T20:22:23Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 20:22, 28 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 12:</td> <td colspan="2" class="diff-lineno">Line 12:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with both domains highlighted:<scene name='56/563200/Native_with_both_domains/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with both domains highlighted:<scene name='56/563200/Native_with_both_domains/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Inhibited with highlighted catalytic:<scene name='56/563200/Rt_inhibited_ac/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Inhibited with highlighted catalytic:<scene name='56/563200/Rt_inhibited_ac/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Inhibited with tyrosine residues:<scene name='56/563200/<del style="color: red; font-weight: bold; text-decoration: none;">Rt_inhibited_ac</del>/<del style="color: red; font-weight: bold; text-decoration: none;">1</del>'>TextToBeDisplayed</scene></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Inhibited with tyrosine residues:<scene name='56/563200/<ins style="color: red; font-weight: bold; text-decoration: none;">Rt_inhibited_with_y_residues</ins>/<ins style="color: red; font-weight: bold; text-decoration: none;">2</ins>'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native tyrosine residues:<scene name='56/563200/Rt_with_y_residues/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native tyrosine residues:<scene name='56/563200/Rt_with_y_residues/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1907509&oldid=prev Student at 20:15, 28 March 2014 2014-03-28T20:15:01Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 20:15, 28 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 11:</td> <td colspan="2" class="diff-lineno">Line 11:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native RNase H:<scene name='56/563200/Native_rnase_h/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native RNase H:<scene name='56/563200/Native_rnase_h/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with both domains highlighted:<scene name='56/563200/Native_with_both_domains/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with both domains highlighted:<scene name='56/563200/Native_with_both_domains/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Inhibited with highlighted catalytic:<scene name='56/563200/<del style="color: red; font-weight: bold; text-decoration: none;">Inhibited_highlighted_cat</del>/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Inhibited with highlighted catalytic:<scene name='56/563200/<ins style="color: red; font-weight: bold; text-decoration: none;">Rt_inhibited_ac/1'>TextToBeDisplayed</scene></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Inhibited with tyrosine residues:<scene name='56/563200/Rt_inhibited_ac/1'>TextToBeDisplayed</scene></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Native tyrosine residues:<scene name='56/563200/Rt_with_y_residues</ins>/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1905383&oldid=prev Student at 16:03, 24 March 2014 2014-03-24T16:03:56Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 16:03, 24 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with highlighted catalytic residues:<scene name='56/563200/Native_with_highligthed_cat/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with highlighted catalytic residues:<scene name='56/563200/Native_with_highligthed_cat/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native RNase H:<scene name='56/563200/Native_rnase_h/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native RNase H:<scene name='56/563200/Native_rnase_h/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Native with both domains highlighted: <scene name='56/563200/Native_with_both_domains/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Native with both domains highlighted:<scene name='56/563200/Native_with_both_domains<ins style="color: red; font-weight: bold; text-decoration: none;">/1'>TextToBeDisplayed</scene></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Inhibited with highlighted catalytic:<scene name='56/563200/Inhibited_highlighted_cat</ins>/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1905381&oldid=prev Student at 15:57, 24 March 2014 2014-03-24T15:57:57Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:57, 24 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 9:</td> <td colspan="2" class="diff-lineno">Line 9:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Reverse transcriptase</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Reverse transcriptase</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with highlighted catalytic residues:<scene name='56/563200/Native_with_highligthed_cat/1'>TextToBeDisplayed</scene></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Native with highlighted catalytic residues:<scene name='56/563200/Native_with_highligthed_cat/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Native RNase H:<scene name='56/563200/Native_rnase_h/1'>TextToBeDisplayed</scene></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Native with both domains highlighted: <scene name='56/563200/Native_with_both_domains/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1905380&oldid=prev Student at 15:44, 24 March 2014 2014-03-24T15:44:41Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:44, 24 March 2014</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the <scene name='56/563200/Phosphofructokinase/1'>secondary structure</scene> 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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the <scene name='56/563200/Phosphofructokinase/1'>secondary structure</scene> 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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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, 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 <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).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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, 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 <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).</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Reverse transcriptase</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Native with highlighted catalytic residues:<scene name='56/563200/Native_with_highligthed_cat/1'>TextToBeDisplayed</scene></div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1852205&oldid=prev Student at 18:42, 15 October 2013 2013-10-15T18:42:57Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:42, 15 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3IE7' size='500' frame='true' align='right' caption='Phosphofructokinase' scene='Insert optional scene name here' /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3IE7' size='500' frame='true' align='right' caption='Phosphofructokinase' scene='Insert optional scene name here' /></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This is the <scene name='56/563200/Phosphofructokinase/1'>secondary structure</scene> of ''Listeria innocua'' Phosphofructokinase, with an associated ATP, several magnesium ions <ins style="color: red; font-weight: bold; text-decoration: none;">(green)</ins>, 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.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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, <del style="color: red; font-weight: bold; text-decoration: none;">and </del>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).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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, the ATP (purple)<ins style="color: red; font-weight: bold; text-decoration: none;">, </ins>and <ins style="color: red; font-weight: bold; text-decoration: none;">the </ins>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).</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_788&diff=1852202&oldid=prev Student at 18:39, 15 October 2013 2013-10-15T18:39:26Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:39, 15 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3IE7' size='500' frame='true' align='right' caption='Phosphofructokinase' scene='Insert optional scene name here' /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3IE7' size='500' frame='true' align='right' caption='Phosphofructokinase' scene='Insert optional scene name here' /></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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. <ins style="color: red; font-weight: bold; text-decoration: none;">Phosphofructokinase is part of the glycolytic pathway. </ins>It <ins style="color: red; font-weight: bold; text-decoration: none;">adds a phosphate group from ATP to fructose 6-phosphate, to form fructose 1,6-bisphosphate.</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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/<del style="color: red; font-weight: bold; text-decoration: none;">3</del>'>ligand interacting <del style="color: red; font-weight: bold; text-decoration: none;">residues</del></scene> that the model displays <del style="color: red; font-weight: bold; text-decoration: none;">all </del>interact with a molecule of glycerol, which is most likely an artifact of the purification and crystallization of the protein. 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 <del style="color: red; font-weight: bold; text-decoration: none;">program does not identify any residues </del>that interact with the ATP <del style="color: red; font-weight: bold; text-decoration: none;">or </del>the <del style="color: red; font-weight: bold; text-decoration: none;">two </del>magnesium ions. The <scene name='56/563200/Active_site/<del style="color: red; font-weight: bold; text-decoration: none;">2</del>'>active site</scene> 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).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Phosphofructokinase </ins>contains 10 <scene name='56/563200/Highlighted_alpha_and_beta/3'>α-helices <ins style="color: red; font-weight: bold; text-decoration: none;">(green) </ins>and 14 β-sheets <ins style="color: red; font-weight: bold; text-decoration: none;">(blue)</ins></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 <ins style="color: red; font-weight: bold; text-decoration: none;">(light blue)</ins></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/<ins style="color: red; font-weight: bold; text-decoration: none;">5</ins>'>ligand interacting <ins style="color: red; font-weight: bold; text-decoration: none;">residures</ins></scene> that the model displays interact with a molecule of glycerol <ins style="color: red; font-weight: bold; text-decoration: none;">(lavender)</ins>, which is most likely an artifact of the purification and crystallization of the protein<ins style="color: red; font-weight: bold; text-decoration: none;">, and the ATP (purple)and magnesium ions(pink)</ins>. 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 <ins style="color: red; font-weight: bold; text-decoration: none;">molecule of ATP has 2 aspartic acids, a glutamic acid, and a lysine </ins>that interact with <ins style="color: red; font-weight: bold; text-decoration: none;">it. There are also a number of uncharged residues that surround </ins>the ATP<ins style="color: red; font-weight: bold; text-decoration: none;">. Proteopedia did not detect any residues within 4 Angstroms of </ins>the magnesium ions. The <scene name='56/563200/Active_site/<ins style="color: red; font-weight: bold; text-decoration: none;">4</ins>'>active site</scene> <ins style="color: red; font-weight: bold; text-decoration: none;">(green) </ins>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).</div></td></tr> </table>

Student