Sandbox Reserved 439: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA, Lynmarie K Thompson, Student

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-=='''YourMacromolecule (pdb)'''==
+=='''Asp Receptor Ligand-binding domain (1wat)'''==
-<StructureSection load='1wat' size='350' side='right' caption='Bacteria use this protein to "smell" their environment, 1wat (PDB entry [[1wat]])' scene=''>
+<StructureSection load='1wat' size='350' side='right' caption='Bacteria use this protein to "smell" their environment (PDB entry [[1wat]])' scene=''>
 by [list all teammate names here]
 [[Student Projects for UMass Chemistry 423 Spring 2016]]
-==Introduction==
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein.
 ==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.
 ==Binding Interactions==
+When the protein is colored according to <scene name='69/695684/Conservation/1'>sequence conservation</scene> , residues at the ligand site are the most conserved.
+{{Template:ColorKey_ConSurf_NoYellow}}
+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='44/443507/Aminohbonds/1'>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>.
 ==Additional Features==
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 Overall Structure - name of team member
-Drug Binding Site - name of team member
+Binding Interactions - name of team member
 Additional Features - name of team member