Sandbox 38
From Proteopedia
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==Basic structural elements== | ==Basic structural elements== | ||
<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | ||
| - | Like many proteins, the <scene name='Sandbox_38/ | + | Like many proteins, the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/12'>secondary structure</scene> of adenylate kinase consists of two elements: alpha-helices (shown in light green) and beta-sheets (shown in dark green). Non-repetitive structural elements are shown in light blue/gray. In addition to the regular hydrogen bonding that causes the secondary structure of the protein, additional <scene name='Sandbox_38/Adenylate_kinase_2o_structure/15'>hydrogen bonding</scene> is present in the backbone of adenylate kinase (shown in yellow), which also contributes to the overall stability/folding of the molecule. |
| - | + | A additional, significant factor in the structural stability/folding of the molecule is the polarity of the amino acid residues. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/16'>hydrophobic</scene> (nonpolar) residues are shown in gray, while the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/17'>hydrophilic</scene> (polar/charged) residues are shown in red. | |
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==Water Accessibility== | ==Water Accessibility== | ||
Revision as of 21:52, 19 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. |
is an enzyme that catalyzes the reaction ATP + AMP = 2ADP. It consists of two identical subunits, A (shown in blue) and B (shown in green). For simplicity's sake, only the A chain will be shown in consequent green links.
Basic structural elements
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Like many proteins, the of adenylate kinase consists of two elements: alpha-helices (shown in light green) and beta-sheets (shown in dark green). Non-repetitive structural elements are shown in light blue/gray. In addition to the regular hydrogen bonding that causes the secondary structure of the protein, additional is present in the backbone of adenylate kinase (shown in yellow), which also contributes to the overall stability/folding of the molecule. A additional, significant factor in the structural stability/folding of the molecule is the polarity of the amino acid residues. The (nonpolar) residues are shown in gray, while the (polar/charged) residues are shown in red.
Water Accessibility
The protein has certain (water shown in blue, the enzyme shown in white), since water can't interact with all of it. Water also interacts with some of the . Waters are and aren't places.
Ligand
Some . Although not all of the highlighted residues contact the ligand, most of them do. Cationic side chains are shown in blue, whereas anionic side chains are shown in red. What kind of side chains interact with non-hydrolysable substrate. The are shown in green.
