Sandbox Reserved 439: Difference between revisions
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[[Student Projects for UMass Chemistry 423 Spring 2016]] | [[Student Projects for UMass Chemistry 423 Spring 2016]] | ||
<StructureSection load='1wat' size='350' side='right' caption='Bacteria use this protein to "smell" their environment (PDB entry [[1wat]])' scene=''> | <StructureSection load='1wat' size='350' side='right' caption='Bacteria use this protein to "smell" their environment (PDB entry [[1wat]])' scene=''> | ||
<font color='orange'>This is an example page. Edit appropriately for your project. Upon completion of each task, delete instructions in orange. See [[Sandbox Reserved 439]] for original instructions</font> | <font color='orange'>This is an example page. Edit appropriately for your project. Upon completion of each task, delete instructions in orange. See [[Sandbox Reserved 439]] for original instructions</font> | ||
<font color='orange'>1. Add a citation to the primary reference at the end of the title above: you should all read this paper! Go to the [http://www.rcsb.org/pdb/home/home.do pdb] and search for your pdb code. Go down to the abstract and click "Search on Pubmed". | <font color='orange'>1. Add a citation to the primary reference at the end of the title above: you should all read this paper! Go to the [http://www.rcsb.org/pdb/home/home.do pdb] and search for your pdb code. Go down to the abstract and click "Search on Pubmed". | ||
In pubmed, copy the PMID code you see right below the abstract, and paste it to replace xxx after PMID in your title (first edited line above).</font> | In pubmed, copy the PMID code you see right below the abstract, and paste it to replace xxx after PMID in your title (first edited line above).</font> | ||
<font color='orange'>2. Each section should start with an "initial view" green scene. These can be the same for all sections or can be set by the section author.Section text should include multiple green scenes and should not exceed the length of the structure window.</font> | <font color='orange'>2. Each section should start with an "initial view" green scene. These can be the same for all sections or can be set by the section author.Section text should include multiple green scenes and should not exceed the length of the structure window.</font> | ||
==Introduction== | ==Introduction== | ||
<font color='orange'>The author of the introduction section should think of a clever/ interesting caption for this structure, and edit to put this caption into the StructureSectionLoad command (4th edited line)</font> | <font color='orange'>The author of the introduction section should think of a clever/ interesting caption for this structure, and edit to put this caption into the StructureSectionLoad command (4th edited line)</font> | ||
The ligand binding domain of the aspartate receptor 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> | |||
==Overall Structure== | ==Overall Structure== | ||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | ||
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== | ||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | ||
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. | 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. | ||
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==Additional Features== | ==Additional Features== | ||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | ||
==Quiz Question 1== | ==Quiz Question 1== | ||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene> | ||