Sandbox 42: Difference between revisions
| Line 9: | Line 9: | ||
The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another. | The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another. | ||
<scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> in gray | The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated. | ||
<scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> in | |||
<scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> in yellow - secondary structure | <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> in yellow - secondary structure | ||
<scene name='Sandbox_42/Wes_-_water-ball_and_stick/1'>Water</scene> in yellow - ball/stick | <scene name='Sandbox_42/Wes_-_water-ball_and_stick/1'>Water</scene> in yellow - ball/stick | ||
<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. | <scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. | ||
<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple | <scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple | ||
Revision as of 02:53, 15 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.
IntroductionAdenylate kinase is a protein that is found in the bacterium yersinia pestis. It consists of two chains, Chain A and Chain B. The two chains are identical and so structural elements can be examined by focusing on one chain. The space filling section of the protein is the ligand, which is bound to the active site in this representation. Structural ElementsThe secondary structure is highlighted here, with alpha helices (shown in green) and beta sheets (blue). Hydrogen bonds are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another. The protein's hydrophobic residues are shown here in stick/wire form, colored gray, while the polar and charged residues are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated. Water in yellow - secondary structure Water in yellow - ball/stick ligand and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. Active site residues in purple |
