Sandbox 32
From Proteopedia
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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. | 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. | ||
| - | The <scene name='Sandbox_32/H_bonds_2/1'>hydrogen bonding</scene> highlighted in this scene shows us that | + | 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. | + | <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. | 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. | ||
Revision as of 01:15, 19 October 2012
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| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
Adenylate Kinase (PDB ID #: 1ake)
The by itself may be in a slightly different conformation than when it is to the B chain (as found in nature).
Adenylate Kinase contains both types of secondary structure, . In this scene, alpha helices are in light blue and beta sheets are in yellow.
The 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.
, 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 , 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.
(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 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 residues are highlighted in red.
