Student Projects for UMass Chemistry 423 Spring 2015: Difference between revisions
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i. See also | i. See also | ||
:All team members should look for related Proteopedia pages (e.g. same protein but with different ligands) and post links here. | :All team members should look for related Proteopedia pages (e.g. same protein but with different ligands) and post links here. | ||
== Example == | |||
This is a complex between a macromolecule and its ligand (but this ligand is not a drug) that illlustrates the use of green scenes: | |||
{{Clear}} | |||
<applet load='1wat' size='[450,338]' frame='true' align='right' | |||
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/> | |||
'''Asp Receptor Ligand-binding domain''' | |||
'''Overall structure''' | |||
The ligand binding domain of the aspartate receptor (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is a dimer of two 4-helix bundles that is shown here with the <scene name='SandboxLKT/Asplabel/2'>aspartate ligand</scene> bound.<ref>PMID: 8486661</ref> In this <scene name='SandboxLKT/Totmhelices/2'>rainbow representation</scene> the <font color='blue'>N</font> and <font color='red'>C</font> termini are at the bottom of the structure; this is where the connections to the transmembrane helices have been truncated. | |||
'''Ligand binding site''' | |||
Interactions that stabilize ligand binding<ref>PMID: 1660187</ref> include hydrogen bonding from Tyr149 and Gln152 backbone carbonyls and Thr154 sidechain OH to the <scene name='SandboxLKT/Asp_ligand_aminohbonds/5'>ligand amino group</scene> and hydrogen bonding from the sidechain nitrogens of Arg64, Arg69, and Arg73 to the two <scene name='SandboxLKT/Asp_ligand_carboxylhbonds/4'>ligand carboxyl groups</scene>. | |||
'''References''' | |||
<references/> | |||
