Group:SMART:2010 Pingry SMART Team: Difference between revisions

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Both NADPH (cofactor) and Testosterone (substrate, not shown) are colored CPK. NADPH can be distinguished by its orange phosphorus atoms.
Both NADPH (cofactor) and Testosterone (substrate, not shown) are colored CPK. NADPH can be distinguished by its orange phosphorus atoms.


<scene name='2010_Pingry_SMART_Team/1lwi_default/5'>The non-polar cavity for substrate binding is colored CPK. Leu54, Tyr55, Trp86, Phe118, Phe129, and Tyr216 are hydrophobic amino acids found in the pocket.</scene> The substrate binding pocket is non-polar because the substrate, testosterone, is a lipid and therefore hydrophobic. This is an important factor when considering how to modify substrate specificity. In Dr. Banta's fuel cell protein, the most common substrate will probably be a sugar, a hydrophilic molecule. In this case, the substrate binding pocket would be polar.  
<scene name='2010_Pingry_SMART_Team/1lwi_default/5'>The non-polar cavity for substrate binding is colored CPK and contains Leu54, Trp86, Phe118, Leu122, Phe128, Phe129, Leu137, and Phe139.</scene> The substrate binding pocket is non-polar because the substrate, testosterone, is a lipid and therefore hydrophobic. This is an important factor when considering how to modify substrate specificity. In Dr. Banta's fuel cell protein, the most common substrate will probably be a sugar, a hydrophilic molecule. In this case, the substrate binding pocket would be polar.  


The catalytic triad, which includes the most important amino acids in regards catalysis, is located at the far end of the pocket.
The catalytic triad, which includes the most important amino acids in regards catalysis, is located at the far end of the pocket.
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{{Clear}}
{{Clear}}
 
====PDB ID: 1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone====  
====PDB ID: 1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone====  
<applet load='1AFS_chainA.pdb' size='400' frame='true' align='left' caption='1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone' scene='2010_Pingry_SMART_Team/1afs_default/7'/>
<applet load='1AFS_chainA.pdb' size='400' frame='true' align='left' caption='1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone' scene='2010_Pingry_SMART_Team/1afs_default/7'/>
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