User:Cody Couperus/Sandbox 1: Difference between revisions

Line 40:

The <scene name='58/583418/A_chain/1'>A chain</scene> is mostly helical and is wound around the B chain and shaped like a boomerang. It is bound to the B chain mostly through side chain interactions including a salt bridge and H-bond cluster at residues D14, E8, and E14c. Furthermore the C-terminus region forms a short amphipathic helix with hydrophobic side chains interacting with the B chain.

The <scene name='58/583418/B_chain/1'>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 beta barrel domains which are surrounded by 4 helical regions and many turns.

The <scene name='58/583418/B_chain/1'>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 active catalytic residues, 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.

@@ Line 40: / Line 40: @@
 The <scene name='58/583418/A_chain/1'>A chain</scene> is mostly helical and is wound around the B chain and shaped like a boomerang. It is bound to the B chain mostly through side chain interactions including a salt bridge and H-bond cluster at residues D14, E8, and E14c. Furthermore the C-terminus region forms a short amphipathic helix with hydrophobic side chains interacting with the B chain.
-The <scene name='58/583418/B_chain/1'>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 beta barrel domains which are surrounded by 4 helical regions and many turns.
+The <scene name='58/583418/B_chain/1'>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 active catalytic residues, 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.