Sandbox 32: Difference between revisions

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==~~This is a placeholder~~==

~~This is a placeholder text to help you get started in~~

~~placing a Jmol applet on your page. At any time, click~~

~~"Show Preview" at the bottom of this page to see how it goes.~~

~~Replace the~~ PDB ~~id (use lowercase!~~) ~~after the STRUCTURE_ and after PDB~~= ~~to load~~

== '''Adenylate Kinase''' (PDB ID #: 1ake)==

~~and display another structure.~~

~~{{STRUCTURE_1a4v | PDB~~=~~1a4v | SCENE~~= }}

The <scene name='Sandbox_32/Chain_a/2'>A Chain</scene> by itself may be in a slightly different conformation than when it is <scene name='Sandbox_32/Both_chains/1'>attached</scene> to the B chain (as found in nature).

Adenylate Kinase contains both types of secondary structure, <scene name='Sandbox_32/Helices_sheets/2'>alpha helices and beta sheets</scene>. In this scene, alpha helices are in light blue and beta sheets are in yellow.

<scene name='Sandbox_32/~~1a4v_secondary_structure~~/1'>~~1a4v secondary structure~~</scene> ~~This model~~ shows the secondary structure of ~~1a4v~~. ~~Alpha helices~~ are shown ~~as magenta rockets~~ and ~~beta sheets~~ are ~~shown as yellow arrows~~. ~~Notice~~ the ~~beta sheets~~ are ~~running~~ in ~~opposite directions~~. (~~anti-parallel~~).

The <scene name='Sandbox_32/H_bonds_2/1'>hydrogen bonding</scene> highlighted in this scene shows us that the secondary structure (helices and sheets) is held together by hydrogen bonds. The beta sheets appear to be parallel, as the H-bonds are not all aligned in one direction.

<scene name='Sandbox_32/Hydrophobic_stickandwireframe/1'>Hydrophobic side chains</scene>, highlighted here in pink, tend to point towards the inside of the molecule where they do not have to interact with the polar water molecules.

The <scene name='Sandbox_32/Hydrophilic/1'>hydrophilic side chains</scene>, highlighted here in blue along with the transparent pink hydrophobic residues, tend to be pointed towards the outside of the protein, where it will interact with the cytosol.

<scene name='Sandbox_32/Water_ligand/3'>Water molecules</scene> (shown in blue) surround and solvate the protein. The ligand is highlighted in green. The waters seem to congregated on one side than the other, possibly to make room for chain B to bind.

Sidechain and ligand <scene name='Sandbox_32/Sidechain_ligand_interaction/2'>interactions</scene> are shown in this scene. The ligand is in orange, and the interacting side chains are in dark blue and red. Of these contacting residues, only some actually catalyze the reaction on the substrate. These <scene name='Sandbox_32/Active_site_2/1'>active site</scene> residues are highlighted in red. These are the residues which interact chemically with the substrate to turn it into product. The non-active site residues are important in substrate (or ligand) binding.

Sandbox 32: Difference between revisions

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-==This is a placeholder==
+<Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /><!-- PLEASE DO NOT DELETE THIS TEMPLATE -->
-This is a placeholder text to help you get started in
+{{Template:Oberholser_Sandbox_Reservation}}
-placing a Jmol applet on your page. At any time, click
+<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-"Show Preview" at the bottom of this page to see how it goes.
-Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
+== '''Adenylate Kinase'''   (PDB ID #: 1ake)==
-and display another structure.
-{{STRUCTURE_1a4v |  PDB=1a4v  |  SCENE=  }}
+The <scene name='Sandbox_32/Chain_a/2'>A Chain</scene> by itself may be in a slightly different conformation than when it is <scene name='Sandbox_32/Both_chains/1'>attached</scene> to the B chain (as found in nature).
+Adenylate Kinase contains both types of secondary structure, <scene name='Sandbox_32/Helices_sheets/2'>alpha helices and beta sheets</scene>.  In this scene, alpha helices are in light blue and beta sheets are in yellow.
-<scene name='Sandbox_32/1a4v_secondary_structure/1'>1a4v secondary structure</scene>   This model shows the secondary structure of 1a4v. Alpha helices are shown as magenta rockets and beta sheets are shown as yellow arrows.  Notice the beta sheets are running in opposite directions.  (anti-parallel).
+The <scene name='Sandbox_32/H_bonds_2/1'>hydrogen bonding</scene> highlighted in this scene shows us that the secondary structure (helices and sheets) is held together by hydrogen bonds.  The beta sheets appear to be parallel, as the H-bonds are not all aligned in one direction.
+<scene name='Sandbox_32/Hydrophobic_stickandwireframe/1'>Hydrophobic side chains</scene>, highlighted here in pink, tend to point towards the inside of the molecule where they do not have to interact with the polar water molecules.
+The <scene name='Sandbox_32/Hydrophilic/1'>hydrophilic side chains</scene>, highlighted here in blue along with the transparent pink hydrophobic residues, tend to be pointed towards the outside of the protein, where it will interact with the cytosol.
+<scene name='Sandbox_32/Water_ligand/3'>Water molecules</scene> (shown in blue) surround and solvate the protein.  The ligand is highlighted in green.  The waters seem to congregated on one side than the other, possibly to make room for chain B to bind.
+Sidechain and ligand <scene name='Sandbox_32/Sidechain_ligand_interaction/2'>interactions</scene> are shown in this scene.  The ligand is in orange, and the interacting side chains are in dark blue and red.  Of these contacting residues, only some actually catalyze the reaction on the substrate.  These <scene name='Sandbox_32/Active_site_2/1'>active site</scene> residues are highlighted in red. These are the residues which interact chemically with the substrate to turn it into product.  The non-active site residues are important in substrate (or ligand) binding.