Sandbox Reserved 439
From Proteopedia
(Difference between revisions)
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| - | ==''' | + | =='''Asp Receptor Ligand-binding domain (1wat)'''== |
| - | <StructureSection load='1wat' size='350' side='right' caption='Bacteria use this protein to "smell" their environment | + | <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] | by [list all teammate names here] | ||
[[Student Projects for UMass Chemistry 423 Spring 2016]] | [[Student Projects for UMass Chemistry 423 Spring 2016]] | ||
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| - | ==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. | ||
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==Overall Structure== | ==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== | ==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}} | ||
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| + | 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== | ==Additional Features== | ||
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Overall Structure - name of team member | Overall Structure - name of team member | ||
| - | + | Binding Interactions - name of team member | |
Additional Features - name of team member | Additional Features - name of team member | ||
Revision as of 18:09, 2 March 2016
| This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439. |
Asp Receptor Ligand-binding domain (1wat)
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