Group:SMART:2010 Pingry SMART Team: Difference between revisions
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====PDB ID: 1lwi, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with NADP+ cofactor==== | ====PDB ID: 1lwi, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with NADP+ cofactor==== | ||
NADPH (cofactor) is colored CPK. | |||
<scene name='2010_Pingry_SMART_Team/1lwi_default/5'>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 catalytic triad is at the distal end of the pocket. | <scene name='2010_Pingry_SMART_Team/1lwi_default/5'>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 catalytic triad is at the distal end of the pocket. | ||
Orange highlights the cofactor specificity sidechains. Gln90, Asn167, Ser166 form hydrogen bonds with the nicotinamide ring. | Orange highlights the cofactor specificity sidechains. Gln90, Asn167, Ser166 form hydrogen bonds with the nicotinamide ring. | ||
Cyan highlights the catalytic triad: Tyr55, Asp50, and Lys84. Tyr55 acts as acid, donates proton to steroid-->Tyr55 forms hydrogen bond to Lys84 to stabilize-->Lys84 forms salt link to Asp50 for further stability | Cyan highlights the catalytic triad: Tyr55, Asp50, and Lys84. Tyr55 acts as acid, donates proton to steroid-->Tyr55 forms hydrogen bond to Lys84 to stabilize-->Lys84 forms salt link to Asp50 for further stability | ||
Dark Gray highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight antiparallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). The top contains two solvent exposed loops (loop A: 116-142 and loop B: 217-235) | Dark Gray highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight antiparallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). The top contains two solvent exposed loops (loop A: 116-142 and loop B: 217-235) | ||
Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B) | Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B) | ||
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====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==== | ||
Testosterone (substrate) and NADPH (cofactor) are colored CPK. | |||
Non-polar cavity for substrate binding is colored CPK. Leu54, Tyr55, Trp86, Phe118, Phe129, and Tyr216 are hydrophobic amino acids found in the pocket. The catalytic triad is at the distal end of the pocket. | |||
Orange highlights the cofactor specificity sidechains. Gln90, Asn167, Ser166 form hydrogen bonds with the nicotinamide ring. | |||
Green highlights the safety belt mechanism in 1AFS. | |||
Cyan highlights the catalytic triad: Tyr55, Asp50, and Lys84. Tyr55 acts as acid, donates proton to steroid-->Tyr55 forms hydrogen bond to Lys84 to stabilize-->Lys84 forms salt link to Asp50 for further stability | |||
Dark Gray highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight antiparallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). The top contains two solvent exposed loops (loop A: 116-142 and loop B: 217-235) | |||
Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B) | |||
{{Clear}} | {{Clear}} | ||
