Sandbox1313: Difference between revisions

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==Lysyl-tRNA Synthase==

Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both ~~"α-~~helices" and ~~"β-strands"~~ (the latter in sheets and a barrel).

Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.

As you can see in the "active site", the lysine participates in multiple "hydrogen bonding interactions" to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome.

As you can see in the "active site", the lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,

~~It is also worth mentioning~~ that ~~when~~ the ~~lysine enters the complex, a small number of~~ "~~residues~~" ~~trigger a~~

<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the synthase. These changes involve "these two loops" and some "other pieces" of the molecule. This conformational change effecively closes the active site when bound to lysine.

~~{{STRUCTURE_1bbw | PDB=1bbw | SCENE= }}~~

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+{{STRUCTURE_1bbw |  PDB=1bbw  |  SCENE=  }}
 ==Lysyl-tRNA Synthase==
-Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both "α-helices" and "β-strands" (the latter in sheets and a barrel).
+Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.
-As you can see in the "active site", the lysine participates in multiple "hydrogen bonding interactions" to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome.
+<applet load='1bbu' size='400' color='white' frame='true' align='left' caption='Lysine-bound lysyl-tRNA synthase' />
+As you can see in the "active site", the lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,
-It is also worth mentioning that when the lysine enters the complex, a small number of "residues" trigger a
+<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the synthase. These changes involve "these two loops" and some "other pieces" of the molecule. This conformational change effecively closes the active site when bound to lysine.
-{{STRUCTURE_1bbw |  PDB=1bbw  |  SCENE=  }}