Sandbox Reserved 1440: Difference between revisions

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This page describes validity of the proposed binding structure at the catalytic triad of the DPP-4 protein. There are a variety of ligands that were tested using electron density clashes and real space R-values to flag potential clashes in the current model.

~~This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.~~

~~You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.~~

== What is a Validation Report? ==

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== 6B1E ==

In the 6B1E protein with resolution 1.77 Å, the big density sizes are far from the ligand, which doesn’t have a significant impact on the binding pocket interaction. All of the missing electron density is not impacting the actual validity of the binding site.

<jmol><jmollink><text>View Figure 1g: 6B1E overview</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/7/7a/6b1e.png";spin on</script></jmollink></jmol>

In the 6B1E crystal structure, the catalytic triad seem to have some missing density but still not significant enough to be an invalid structure and interaction with the LF7 ligand.

<jmol><jmollink><text>View Figure 1g: 6B1E Triad Density</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/6/6e/6b1e_density.png";spin on</script></jmollink></jmol>

== 4N8D ==

Sandbox Reserved 1440: Difference between revisions

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 <StructureSection load='1nu6' size='340' side='right' caption='The 1nu6 DPP-4 binding' scene=''>
 This page describes validity of the proposed binding structure at the catalytic triad of the DPP-4 protein.  There are a variety of ligands that were tested using electron density clashes and real space R-values to flag potential clashes in the current model.
-This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
 == What is a Validation Report? ==
@@ Line 63: / Line 61: @@
 == 6B1E ==
+In the 6B1E protein with resolution 1.77 Å, the big density sizes are far from the ligand, which doesn’t have a significant impact on the binding pocket interaction. All of the missing electron density is not impacting the actual validity of the binding site.
+<jmol><jmollink><text>View Figure 1g: 6B1E overview</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/7/7a/6b1e.png";spin on</script></jmollink></jmol>
+In the 6B1E crystal structure, the catalytic triad seem to have some missing density but still not significant enough to be an invalid structure and interaction with the LF7 ligand.
+<jmol><jmollink><text>View Figure 1g: 6B1E Triad Density</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/6/6e/6b1e_density.png";spin on</script></jmollink></jmol>
 == 4N8D ==