User:Cody Couperus/Sandbox 1: Difference between revisions

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The <scene name='58/583418/B_chain/1' target='0'>B chain</scene> contains the active site of the protein and has numerous notable structural features. The active site is formed at the rims of two interacting 6 stranded <scene name='58/583418/Beta_barrel/1'>beta barrel domains</scene> which are surrounded by 4 helical regions and many turns.

The serine protease <scene name='58/583418/Catalytic_triad/1~~' target='0~~'>~~catalytic triad~~</scene>, based on chymotrypsin numbering, are Ser195, His57, and Asp102. As is common with serine proteases, an oxanion hole is formed by backbone amides of Ser195 and Gly193. This has the functional role of stabilizing the oxanion intermediate involved in the serine protease mechanism. In addition, since thrombin cleaves after Arg/Lys the S1 specificity site, formed by the 180s- and 220s- loops, has Asp189 at the base to form a salt bridge with the incoming substrate. Furthermore, the S4 binding pocket accommodates hydrophobic substrate residues.

The serine protease <scene name='58/583418/Catalytic_triad/1'>TextToBeDisplayed</scene>, based on chymotrypsin numbering, are Ser195, His57, and Asp102. As is common with serine proteases, an oxanion hole is formed by backbone amides of Ser195 and Gly193. This has the functional role of stabilizing the oxanion intermediate involved in the serine protease mechanism. In addition, since thrombin cleaves after Arg/Lys the S1 specificity site, formed by the 180s- and 220s- loops, has Asp189 at the base to form a salt bridge with the incoming substrate. Furthermore, the S4 binding pocket accommodates hydrophobic substrate residues.

The '''active site''' cleft rims are formed by the hydrophobic and rigid <scene name='58/583418/Loops/1'>60-loops</scene> (residues L60, Y60a, P60b, P60c, W60d, D60e, K60f, N60g, F60h, T60i, and N60g) and the <scene name='58/583418/Loops/1'>γ-loop</scene> (residues T147, W147a, T147b, A147c, N147d, and V147f) while the base is mostly hydrophilic negatively charged amino acids. The cleft is deep compared to more promiscuous serine proteases, consequently substrates must either have a large loop that is cleaved or have favorable interactions with the insertion loops <ref>PMID: 16102053</ref>.

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 The <scene name='58/583418/B_chain/1' target='0'>B chain</scene> contains the active site of the protein and has numerous notable structural features. The active site is formed at the rims of two interacting 6 stranded <scene name='58/583418/Beta_barrel/1'>beta barrel domains</scene> which are surrounded by 4 helical regions and many turns.
-The serine protease <scene name='58/583418/Catalytic_triad/1' target='0'>catalytic triad</scene>, based on chymotrypsin numbering, are Ser195, His57, and Asp102. As is common with serine proteases, an oxanion hole is formed by backbone amides of Ser195 and Gly193. This has the functional role of stabilizing the oxanion intermediate involved in the serine protease mechanism. In addition, since thrombin cleaves after Arg/Lys the S1 specificity site, formed by the 180s- and 220s- loops, has Asp189 at the base to form a salt bridge with the incoming substrate. Furthermore, the S4 binding pocket accommodates hydrophobic substrate residues.
+The serine protease <scene name='58/583418/Catalytic_triad/1'>TextToBeDisplayed</scene>, based on chymotrypsin numbering, are Ser195, His57, and Asp102. As is common with serine proteases, an oxanion hole is formed by backbone amides of Ser195 and Gly193. This has the functional role of stabilizing the oxanion intermediate involved in the serine protease mechanism. In addition, since thrombin cleaves after Arg/Lys the S1 specificity site, formed by the 180s- and 220s- loops, has Asp189 at the base to form a salt bridge with the incoming substrate. Furthermore, the S4 binding pocket accommodates hydrophobic substrate residues.
 The '''active site''' cleft rims are formed by the hydrophobic and rigid <scene name='58/583418/Loops/1'>60-loops</scene> (residues L60, Y60a, P60b, P60c, W60d, D60e, K60f, N60g, F60h, T60i, and N60g) and the <scene name='58/583418/Loops/1'>γ-loop</scene> (residues T147, W147a, T147b, A147c, N147d, and V147f) while the base is mostly hydrophilic negatively charged amino acids. The cleft is deep compared to more promiscuous serine proteases, consequently substrates must either have a large loop that is cleaved or have favorable interactions with the insertion loops <ref>PMID: 16102053</ref>.