Sandbox 31: Difference between revisions
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<Structure load='1ake' size='500' frame='true' align='right' caption=' | == '''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' /> | |||
==Introduction== | ==Introduction== | ||
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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> | |||
