Sandbox 31: Difference between revisions
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== '''Adenylate Kinase''' (PDB ID #: 1ake)== | == '''Adenylate Kinase''' (PDB ID #: 1ake)== | ||
<Structure load='1ake' size='500' frame='true' align='right' caption='adenylate kinase bound to non-hydrolyzable substrate analogue' scene='Insert optional scene name here' /> | <Structure load='1ake' size='500' frame='true' align='right' caption='adenylate kinase bound to non-hydrolyzable substrate analogue' scene='Insert optional scene name here' /> | ||
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==Physical Properties== | ==Physical Properties== | ||
Adenylate kinase is caged with <scene name='Sandbox_31/Ak_waters/1'>water molecules</scene>. | |||
==I can add headings== | |||
This is the <scene name='Sandbox_31/Ak_main/1'>AK</scene> scene. | |||
==Structure== | ==Structure== | ||
The <scene name='Sandbox_31/Ak_secondary_structure/1'>secondary structure</scene> of adenylate kinase shows alpha | The <scene name='Sandbox_31/Ak_secondary_structure/1'>secondary structure</scene> of adenylate kinase shows alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange). A network of <scene name='Sandbox_31/Ak_hydrogen_bonds/1'>hydrogen bonds</scene> hold the secondary structural elements together. You can see the regular hydrogen bonding pattern in the alpha helices. | ||
Adenylate kinase has a <scene name='Sandbox_31/Ak_hydrophilic/1'>hydrophilic</scene> exterior, and a <scene name='Sandbox_31/Ak_hydrophobic/1'>hydrophobic</scene> core, with additional | |||
<scene name='Sandbox_31/Ak_hydrophilic_hydrophobic/1'>hydrophilic residues</scene> on the interior contacting the ligand. | <scene name='Sandbox_31/Ak_hydrophilic_hydrophobic/1'>hydrophilic residues</scene> on the interior contacting the ligand. | ||
<scene name='Sandbox_31/Ak_2nd_structure/1'>helix and sheet</scene> | |||
==Active Site and Mechanism== | ==Active Site and Mechanism== | ||
residues within <scene name='Sandbox_31/Ak_ligand_binding/3'>3 angstroms</scene> of the ligand are involved in binding the ligand or stabilizing the active site. | residues within <scene name='Sandbox_31/Ak_ligand_binding/3'>3 angstroms</scene> of the ligand are involved in binding the ligand or stabilizing the active site. | ||
adenylate kinase's <scene name='Sandbox_31/Ak_active_site/1'>active site</scene> is highlighted in dark blue. | |||
together you can see that the <scene name='Sandbox_31/Ak_ligand_binding_and_active_s/1'>active site</scene> is only a fraction of the molecules involved in binding the ligand. | |||
<Structure load='3be4' size='500' frame='true' align='right' caption='Cryptosporidium parvum' scene='adenylate kinase' /> | |||
Comparing the E.coli structure to <scene name='Sandbox_31/Ak_cryptosporidium_parvum/1'>Cryptosporidium parvum</scene> | |||
==References== | ==References== | ||
<references/> | <references/> | ||
<scene name='Sandbox_31/Rhodopsin_ball_and_chain/1'>Rhodopsin ball and stick</scene> | |||
Latest revision as of 17:02, 26 November 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.
Adenylate Kinase (PDB ID #: 1ake)
IntroductionAdenylate Kinase is a good little protein.
Physical PropertiesAdenylate kinase is caged with water molecules. I can add headingsThis is the AK scene. StructureThe secondary structure of adenylate kinase shows alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange). A network of hydrogen bonds hold the secondary structural elements together. You can see the regular hydrogen bonding pattern in the alpha helices. Adenylate kinase has a hydrophilic exterior, and a hydrophobic core, with additional hydrophilic residues on the interior contacting the ligand. Active Site and Mechanismresidues within 3 angstroms of the ligand are involved in binding the ligand or stabilizing the active site. adenylate kinase's active site is highlighted in dark blue. together you can see that the active site is only a fraction of the molecules involved in binding the ligand.
Comparing the E.coli structure to Cryptosporidium parvum References |
