Sandbox 48
From Proteopedia
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The <scene name='Sandbox_48/Secondary__structure__greenblu/1'>secondary structures</scene> of Chain A of adenylate kinase includes alpha-helices (green), and beta-sheets (blue). The location of the <scene name='Sandbox_48/2_structure_hbondson/1'>hydrogen bonds</scene> within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded. | The <scene name='Sandbox_48/Secondary__structure__greenblu/1'>secondary structures</scene> of Chain A of adenylate kinase includes alpha-helices (green), and beta-sheets (blue). The location of the <scene name='Sandbox_48/2_structure_hbondson/1'>hydrogen bonds</scene> within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded. | ||
| - | Within these structures the <scene name='Sandbox_48/Secondary__structure__hydropho/1'>hydrophobic</scene> residues are located closest on the inside of the enzyme. The <scene name='Sandbox_48/Secondary__structure__hydrophi/1'>hydrophillic | + | Within these structures the <scene name='Sandbox_48/Secondary__structure__hydropho/1'>hydrophobic</scene> residues (purple) are located closest on the inside of the enzyme. The <scene name='Sandbox_48/Secondary__structure__hydrophi/1'>hydrophillic </scene> residues (charged and polar) are on the outward face of the enzyme. |
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== Solvent Accessibility == | == Solvent Accessibility == | ||
Revision as of 01:17, 18 October 2012
| 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. |
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Secondary Structure in Chain A
We will be examining the structure of
The of Chain A of adenylate kinase includes alpha-helices (green), and beta-sheets (blue). The location of the within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded.
Within these structures the residues (purple) are located closest on the inside of the enzyme. The residues (charged and polar) are on the outward face of the enzyme.
Solvent Accessibility
To assess the solvent accessibility of adenylate kinase, (purple) are shown on the molecule. These are the spaces in the protein that are capable of being accessed by solvent. Solvent accumulates near the center of the molecule, and is found on the outward chains like the alpha helices. The ligand (green) is highlighted to show that the water molecules surround the ligand in the middle of the ligand, but not by the ends.
Ligand Interaction
There are charged residues that , or make up the interaction site. The positively charged (blue) residues of the enzyme interact with the negatively charged (red) residues of the ligand.
