Sandbox Reserved 1440

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1NU6 protein along with the ligand and catalytic triad displayed. The data was captured with a 2.10 Å resolution. The ligand NDG is not found in the binding site, rather it is bound to the outside of the binding pocket. This indicates that the ligand may be binding to an allosteric site and modulating the activity at the binding site. The ligands present in this model are two sugars (NAD and NDG), a Mercury (II) ion, and water. Of these, the mercury ion is closest to the triad, but is not close enough to represent a binding interaction. NDG however is found near the opening of the binding pocket, and thus may be an allosteric site for the protein.
1NU6 protein along with the ligand and catalytic triad displayed. The data was captured with a 2.10 Å resolution. The ligand NDG is not found in the binding site, rather it is bound to the outside of the binding pocket. This indicates that the ligand may be binding to an allosteric site and modulating the activity at the binding site. The ligands present in this model are two sugars (NAD and NDG), a Mercury (II) ion, and water. Of these, the mercury ion is closest to the triad, but is not close enough to represent a binding interaction. NDG however is found near the opening of the binding pocket, and thus may be an allosteric site for the protein.
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<Structure load='1nu6' size='350' frame='true' align='right' caption='The 1NU6 DPP-4 Protein' scene='Insert optional scene name here' />
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The catalytic triad of the protein is shown here. Important to note that there are no clashes surrounding the site, and thus the model may provide an accurate representation of the binding capabilities of this binding pocket.
The catalytic triad of the protein is shown here. Important to note that there are no clashes surrounding the site, and thus the model may provide an accurate representation of the binding capabilities of this binding pocket.
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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. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==
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<references/>
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Please note this way for '''referencing a paper''' using the PubmedID <ref>pmid 22437502</ref>. The full reference appears at the bottom of the page.
 
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[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
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== Authors ==
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doi:10.1038/nature10954]
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<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
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Lana Jevtic, Kaeli Jacobson, Tayler Aarness, Eric Ruterbories.
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<jmol><jmollink><text>View Figure 1a: Overall view of the µ-OR structure</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/6/6b/1nu6_pocket.png"</script></jmollink></jmol>
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St. Olaf College.
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Shown in Figure 1a is a close-up view of a morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]) bound to the µ-opioid receptor. The green circles indicate hydrogen bonds.
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Medicinal Chemistry, Interim 2018.
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<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>
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Professor Robert Hanson.
</StructureSection>
</StructureSection>
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<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
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code for the above (space inserted just after the : <code>&lt;jmol><jmollink><text>View Figure 1a: Overall view of the µ-OR structure</text><script>exit;figure=1;SCRIPT "/wiki/images/8/8b/4dkl-local-contact.png"</script></jmollink></jmol></code>
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<jmol><jmollink><text>View Figure 1b: 1NU6</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/6/6b/1nu6_pocket.png"</script></jmollink></jmol>
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Shown in Figure 1a is a close-up view of a morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]) bound to the µ-opioid receptor. The green circles indicate hydrogen bonds.
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<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>
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<references/>
 
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== Authors ==
 
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Lana Jevtic, Kaeli Jacobson, Tayler Aarness, Eric Ruterbories.
 
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St. Olaf College.
 
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Medicinal Chemistry, Interim 2018.
 
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Professor Robert Hanson.
 
</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Revision as of 18:52, 29 January 2018

This Sandbox is Reserved from 5 Jan through 7 Feb, 2018 for use in the course Medicinal Chemistry taught by Bob Hanson at the St. Olaf College, Northfield, MN. This reservation includes Sandbox Reserved 1431 through Sandbox Reserved 1445.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
  • Click the 3D button (when editing, above the wikitext box) to insert Jmol.
  • show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
  • Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

Validation of the Binding Action at the DPP-4 Protein

The 1nu6 DPP-4 binding

Drag the structure with the mouse to rotate

Click a green link on the left to load Figure 1

Drag the structure with the mouse to rotate

References

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