Proteopedia - User contributions [en]

File:1crn-test.pdb

2024-08-14T15:33:57Z

Bob Hanson: testing

testing

File:Met Atom Names Dist.pse

2024-07-17T13:48:22Z

Bob Hanson: test with atom names

test with atom names

User:Bob Hanson/Sandbox 1

2024-07-15T14:48:49Z

Bob Hanson: /* all about adamantane */

==all about adamantane==
testing here

<StructureSection load='' size='350' frame='true' side='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>

this is a test

<scene name='91/919062/Pse_test/1'>psetest1</scene>

<scene name='91/919062/Bhtestgol/1'>gol.pse from reload</scene>

An example of using unaltered PNGJ files, <jmol><jmolLink>
<script>
load /wiki/images/a/a0/Histamine_-_Copy.png
</script>
<text>click here to see</text>
</jmolLink></jmol> how it looks.

</StructureSection>

File:GolBinding2.pse

2024-07-15T14:41:31Z

Bob Hanson: uploaded a new version of "Image:GolBinding2.pse": bh gol test

gol binding test

File:GolBinding2.pse

2024-07-15T14:40:51Z

Bob Hanson: gol binding test

gol binding test

File:Gol Binding.pse

2024-07-15T14:36:00Z

Bob Hanson: uploaded a new version of "Image:Gol Binding.pse": updated gol_binding.pse

User:Bob Hanson/Sandbox 1

2024-07-15T13:14:58Z

Bob Hanson: /* all about adamantane */

==all about adamantane==
testing here

<StructureSection load='' size='350' frame='true' side='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>

this is a test

<scene name='91/919062/Pse_test/1'>TextToBeDisplayed</scene>

An example of using unaltered PNGJ files, <jmol><jmolLink>
<script>
load /wiki/images/a/a0/Histamine_-_Copy.png
</script>
<text>click here to see</text>
</jmolLink></jmol> how it looks.

</StructureSection>

User:Bob Hanson/Sandbox 1

2024-07-15T13:14:29Z

Bob Hanson: Undo revision 4190882 by Bob Hanson (Talk)

==all about adamantane==
testing here

<StructureSection load='' size='350' frame='true' side='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>

this is a test

<scene name='91/919062/Blue_adamantane_2/1'>TextToBeDisplayed</scene>

An example of using unaltered PNGJ files, <jmol><jmolLink>
<script>
load /wiki/images/a/a0/Histamine_-_Copy.png
</script>
<text>click here to see</text>
</jmolLink></jmol> how it looks.

</StructureSection>

User:Bob Hanson/Sandbox 1

2024-07-15T13:12:29Z

Bob Hanson:

<scene name='91/919062/Pse_test/1'>TextToBeDisplayed</scene>

File:Bhtest.pse

2024-07-15T13:03:32Z

Bob Hanson:

User:Bob Hanson/Sandbox 1

2022-08-06T17:06:42Z

Bob Hanson:

==all about adamantane==
testing here

<StructureSection load='' size='350' frame='true' side='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>

this is a test

<scene name='91/919062/Blue_adamantane_2/1'>TextToBeDisplayed</scene>

An example of using unaltered PNGJ files, <jmol><jmolLink>
<script>
load /wiki/images/a/a0/Histamine_-_Copy.png
</script>
<text>click here to see</text>
</jmolLink></jmol> how it looks.

</StructureSection>

User:Bob Hanson/Sandbox 2

2022-08-05T19:06:03Z

Bob Hanson:

==all about adamantane==
testing here

<StructureSection load='' size='350' height='500' frame='true' align='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>

this is a test

An example of using unaltered PNGJ files, <jmol><jmolLink>
<script>
load /wiki/images/a/a0/Histamine_-_Copy.png
</script>
<text>click here to see</text>
</jmolLink></jmol> how it looks.

</StructureSection>
== References ==
<references/>

User:Bob Hanson/Sandbox 2

2022-08-05T19:05:27Z

Bob Hanson: New page: ==all about adamantane== testing here <StructureSection load='' size='350' frame='true' align='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'> this is a test ...

==all about adamantane==
testing here

<StructureSection load='' size='350' frame='true' align='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>

this is a test

An example of using unaltered PNGJ files, <jmol><jmolLink>
<script>
load /wiki/images/a/a0/Histamine_-_Copy.png
</script>
<text>click here to see</text>
</jmolLink></jmol> how it looks.

</StructureSection>
== References ==
<references/>

User:Bob Hanson/Sandbox 1

2022-08-05T18:53:36Z

Bob Hanson:

==all about adamantane==
testing here

<StructureSection load='' size='350' frame='true' align='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>

this is a test

<scene name='91/919062/Blue_adamantane_2/1'>TextToBeDisplayed</scene>

An example of using unaltered PNGJ files, <jmol><jmolLink>
<script>
load /wiki/images/a/a0/Histamine_-_Copy.png
</script>
<text>click here to see</text>
</jmolLink></jmol> how it looks.

</StructureSection>

User:Bob Hanson/Sandbox 1

2022-08-05T13:45:46Z

Bob Hanson:

User:Bob Hanson/Sandbox 1

2022-08-05T13:33:33Z

Bob Hanson:

User:Bob Hanson/Sandbox 1

2022-08-05T13:28:42Z

Bob Hanson: /* all about adamantane */

==all about adamantane==
testing here

<Structure load='Adamantane.mol' size='350' frame='true' align='right' caption='Insert caption here' </structure>
this is a test
<scene name='91/919062/Blue_adamantane/1'>blue</scene>

User:Bob Hanson/Sandbox 1

2022-08-05T13:28:03Z

Bob Hanson:

==all about adamantane==
testing here

<Structure load='Adamantane.mol' size='350' frame='true' align='right' caption='Insert caption here'>

this is a test
<scene name='91/919062/Blue_adamantane/1'>blue</scene>

</structure>

User:Bob Hanson/Sandbox 1

2022-08-05T13:25:07Z

Bob Hanson:

==all about adamantane==

<Structure load='Adamantane.mol' size='350' frame='true' align='right' caption='Insert caption here'>
<scene name='91/919062/Blue_adamantane/1'>Text To Be Displayed</scene>

</structure>

User:Bob Hanson/Sandbox 1

2022-08-05T13:06:13Z

Bob Hanson: /* all about adamantane */

==all about adamantane==

<Structure load='Adamantane.mol' size='350' frame='true' align='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1' />

User:Bob Hanson/Sandbox 1

2022-08-05T13:04:59Z

Bob Hanson: /* all about adamantane */

==all about adamantane==

<Structure load='blue_adamantane.mol' size='350' frame='true' align='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1' />

User:Bob Hanson/Sandbox 1

2022-08-05T13:02:12Z

Bob Hanson:

==all about adamantane==
<structure>
<scene name='91/919062/Blue_adamantane/1'>Adamantane</scene>

</structure>

User:Bob Hanson/Sandbox 1

2022-08-05T13:01:40Z

Bob Hanson:

==all about adamantane==

<scene name='91/919062/Blue_adamantane/1'>Adamantane</scene>

User:Bob Hanson/Sandbox 1

2022-08-05T13:00:14Z

Bob Hanson: /* Your Heading Here (maybe something like 'Structure') */

File:Adamantane.mol

2022-08-05T12:55:09Z

Bob Hanson:

User:Bob Hanson/Sandbox 1

2022-08-05T12:53:52Z

Bob Hanson:

User:Bob Hanson/Sandbox 1

2022-08-05T12:53:04Z

Bob Hanson: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Bob Hanson/Sandbox 1'''. 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.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

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.

</StructureSection>
== References ==
<references/>

User:Bob Hanson

2022-08-05T12:52:11Z

Bob Hanson:

* Full Real Name: Bob Hanson

* Position: Professor of Chemistry

* Institution (NO ABBREVIATIONS): Saint Olaf College

* City, State/Province, Country: Northfield, MN, USA

* Field of Expertise or Study: Organic Chemistry, Jmol, molecular visualization

*[[User:Bob Hanson/Sandbox 1]]

File:Histamine - Copy.png

2022-08-04T17:05:22Z

Bob Hanson: test histamine as PNG extension

test histamine as PNG extension

Sandbox Reserved 1431

2018-01-31T01:03:23Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
see [https://www.nature.com/articles/nature10954 the paper] for essentially this exact figure.

Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor on the endocellular (inside the cell) side. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure after loading the <jmol><jmollink><text>Figure 1 model</text><script>exit;SCRIPT "http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png"</script></jmollink></jmol> by dragging it around using your mouse or clicking the buttons below. SHIFT-drag to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure}; SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

BELOW THIS LINE IS NOT PART OF THE ACTUAL PAGE

code for the above (space inserted just after the : <code><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>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-31T01:02:41Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
see [https://www.nature.com/articles/nature10954 for essentially this exact figure]

Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor on the endocellular (inside the cell) side. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure after loading the <jmol><jmollink><text>Figure 1 model</text><script>exit;SCRIPT "http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png"</script></jmollink></jmol> by dragging it around using your mouse or clicking the buttons below. SHIFT-drag to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure}; SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

BELOW THIS LINE IS NOT PART OF THE ACTUAL PAGE

code for the above (space inserted just after the : <code><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>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1440

2018-01-30T15:48:56Z

Bob Hanson:

==Validation of the Binding Action at the DPP-4 Protein==
<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.

== What is a Validation Report? ==

A validation report (see linked image) [[http://proteopedia.org//wiki/images/d/df/RSRZ_validation.png]] is an analysis of a molecular dataset model and the real space electron density of the proposed model. There are several factors that affect the validity of the model. Perhaps the most important is the resolution in Angstroms. A low resolution of less than 2 will likely have few electron density clashes, while a resolution of above 3 will have several clashes due to overlapping atomic radii.

Validaton report guidelines.
<b>Rfree</b> - measures the fit of the model using a subset of the data available.

<b>RSRZ outliers</b> - Real Space R values, measures fit of atomic model vs. the collected data in real space.

<b>Clashscore</b> - Derived from number of atoms in the model that are unusually close together.

<b>Ramachandran outliers</b> - Measures φ (phi) and ψ (psi) angle irregularities.

<b>Sidechain outliers</b> - Measures protein sidechain outliers and deviations from expected backbone angles.

== JMol Images ==

This page will allow the user to view Jmol renderings of each protein along with the ligand in the binding pocket. The validation report will also identify the clashes in the model, which will be indicated as follows:

<font color="red">Red atoms</font> indicate that there are significant clashes in the area of the displayed atom

<font color="blue">Blue atoms</font> indicate that there are less significant but still present clashes in the area of the displayed atom.

Overall <font color="blue">Blue</font> indicates a minor issue, while <font color="red">Red </font> indicates a major discrepancy between the measured electron density and the location in the model.

The magnitude of any clashes are also indicated with the size of the atom where <font size="5">BIG </font> atoms indicate a larger clash than <font size="1"> small </font> atoms.

== 3Q8W ==

Outside view of 3Q8W binding pocket (orange) with clashes shown
http://proteopedia.org/wiki/images/9/9b/3Q8W_Clash_Outside.png

3Q8W is the structure with the worst resolution (3.64 Å), but the majority of the structure’s validation issues are due to its large clashscore. It has little to no RSRZ issues. The structure itself is valid, although its resolution is poor.

Click to see catalytic triad of 3Q8W: [[http://proteopedia.org/wiki/images/1/12/3Q8W_Clashes_Triad.png]]

== 1NU6 ==

<jmol><jmollink><text>View Figure 1a: 1NU6 overview</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/d/d2/1nu6_B.png";spin on</script></jmollink></jmol>

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.

<jmol><jmollink><text>View Figure 1b: 1NU6 Triad</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/d/d2/1nu6_B.png";zoomto *4</script></jmollink></jmol>

The catalytic triad of the protein is shown in Figure 1b. 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.

== 1PFQ ==

Image of the 1PFQ binding pocket and surrounding clashes

http://proteopedia.org/wiki/images/9/9a/1PFQ_RSRZ_bwr.png

1PFQ has the highest number of RSRZ issues and a resolution of 1.9 Å. However, the largest gaps in electron density are located on the edges of the protein (red), and the majority of the gaps are relatively small (blue).

1PFQ’s binding pocket is surrounded by gaps in the electron density data. The residues of the catalytic triad do not have any missing data. Therefore, while the overall structure of 1PFQ isn’t particularly accurate, studies focusing on the catalytic triad should have accurate data.

Click to see the catalytic triad: [[http://proteopedia.org/wiki/images/7/75/1PFQ_RSRZ_Triad.png]]

== 5T4B ==

5T4B has a resolution of 1.76 Å and can be seen here with the 75N ligand within the binding pocket. There are more RSRZ outliers near the entrance to the binding cavity, but few clashes near the actual binding site. This indicates that the binding pocket itself has validity, but the mechanism for the ligand entering the cavity may be in question.

<jmol><jmollink><text>View Figure 1c: 5T4B</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/a/a4/5t4b_A.png";spin on</script></jmollink></jmol>

Shown in Figure 1c is a view of a the 75N ligand inside the binding pocket of DPP-4.

The 5T4B catalytic triad shown with electron density around the SER630, HIS740 and ASP706 residuals. There are no clashes at the triad.

To see the binding pocket of the 75N ligand at the catalytic triad, click on Figure 1d. There is electron density from the catalytic triad that extends into the binding pocket, and surrounding the functional binding groups on the ligand. No RSRZ outliers are found within the binding pocket, and this conformation of the molecule is supported by the electron density surrounding the catalytic triad.

<jmol><jmollink><text>View Figure 1d: 5T4B</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/a/a4/5t4b_A.png";zoomto *5</script></jmollink></jmol>

== 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.

Figure 1g: Broad view of the 6B1E binding

http://proteopedia.org/wiki/images/7/7a/6b1e.png

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.

Figure 1h: View of the 6B1E catalytic triad

http://proteopedia.org/wiki/images/6/6e/6b1e_density.png

== 4N8D ==

4N8D with resolution 1.65 Å: an overview of the binding site, missing densities, and clashes. Overall, the missing density sizes are not significant, which gives this crystal a valid structure. And the clashscore is not high, which means it’s not conflicting with the binding site. This crystal seems to be less valid than 6B1E in terms of the RSRZ score, but not enough to be claimed an invalid structure.

<jmol><jmollink><text>View Figure 1d: 4N8D overview</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/0/00/4n8d_D.png";spin on</script></jmollink></jmol>

4N8D: the catalytic triads missing densities are shown. The densities of the amino acids are not significant enough to be viewed as an invalid structure, but does have more missing than the 6B1E crystal.

Catalytic triad: [[http://proteopedia.org/wiki/images/0/06/6b1eeeeejsmol.png]]

== 4A5S ==

Broad view of 4A5S molecule with binding pocket and clashes

http://proteopedia.org/wiki/images/7/79/4A5S_RSRZ_Full.png

4A5S has the highest resolution of all of the DPP4 structures at 1.62 Å. It has a relatively low amount of RSRZ issues, although the gaps are larger. Also, its RSRZ issues are generally only around the edges of the protein chain.

There are no clashes around the binding pocket [[http://proteopedia.org/wiki/images/4/4d/4A5S_RSRZ_Triad.png]], meaning this should be an accurate model. Also the electron density doesn’t show any gaps.

== Structural highlights ==

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.

<references/>

== Authors ==

Lana Jevtic, Kaeli Jacobson, Tayler Aarness, Eric Ruterbories.

St. Olaf College.

Medicinal Chemistry, Interim 2018.

Professor Robert Hanson.

</StructureSection>

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>

<jmol><jmollink><text>View Figure 1b: 1NU6</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/0/0b/1nu6_pocket2.png";spin on</script></jmollink></jmol>

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.

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1442

2018-01-30T12:47:21Z

Bob Hanson: /* Dipeptidyl Peptidase IV (DPP-IV) */

==Dipeptidyl Peptidase IV (DPP-IV)==

'''Active Site of Dipeptidyl Peptidase IV (DPP-IV)'''

<StructureSection load='1nu6' size='340' side='right' caption='Dipeptidyl Peptidase IV' scene=''>

The DPP-IV active site exists at the intersection of a α/β hydrolase domain and a β-propeller domain and consists of the catalytic triad and supporting residues. The catalytic triad is made up of a nucleophile, Serine630, a base, Histidine740, and an acid, Aspartate708. Also essential to the cleaving mechanism are two supporting residues, Tyr547 and Tyr631, that stabilize the oxyanion tetrahedral intermediate by forming hydrogen bonds with the oxyanion. In addition, there are anchoring residues that coordinate the carbonyl of the N-terminal amino acid residue of the substrate and align it for the nucleophilic attack by Ser630. These residues are Glu205, Glu206, Asn710, and Arg125.

<jmol><jmollink><text>View Figure 1a: Overall view of the µ-OR structure</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/a/a6/Animation1.png"</script></jmollink></jmol>

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.

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/12/Transition2.spt"</script></jmollink></jmol>

</StructureSection>

<references/>

Sandbox Reserved 1442

2018-01-30T12:45:13Z

Bob Hanson:

Sandbox Reserved 1431

2018-01-30T12:24:15Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor on the endocellular (inside the cell) side. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure after loading the <jmol><jmollink><text>Figure 1 model</text><script>exit;SCRIPT "http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png"</script></jmollink></jmol> by dragging it around using your mouse or clicking the buttons below. SHIFT-drag to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure}; SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>if (!figure){figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure};SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

BELOW THIS LINE IS NOT PART OF THE ACTUAL PAGE

code for the above (space inserted just after the : <code><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>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-30T03:47:51Z

Bob Hanson:

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor on the endocellular (inside the cell) side. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure after loading the <jmol><jmollink><text>Figure 1 model</text><script>exit;SCRIPT "http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png"</script></jmollink></jmol> by dragging it around using your mouse or clicking the buttons below. SHIFT-drag to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-30T02:41:57Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure after loading the <jmol><jmollink><text>Figure 1 model</text><script>exit;SCRIPT "http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png"</script></jmollink></jmol> by dragging it around using your mouse or clicking the buttons below. SHIFT-drag to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-30T02:40:43Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure after loading the <jmol><jmollink><text>figure</text><script>exit;SCRIPT "http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png"</script></jmollink></jmol> by dragging it around using your mouse or clicking the buttons below. SHIFT-drag to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-30T02:40:09Z

Bob Hanson:

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure after downloading the <jmol><jmollink><text>figure</text><script>exit;SCRIPT "http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png"</script></jmollink></jmol> by dragging it around using your mouse or clicking the buttons below. SHIFT-drag to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-30T02:37:27Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

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.

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure by dragging it around using your mouse or clicking the buttons below. Press SHIFT to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/0/00/Nature10954_fig1d.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

File:Nature10954 fig1d.spt

2018-01-30T02:35:33Z

Bob Hanson:

File:Nature10954 fig1c.spt

2018-01-30T02:34:44Z

Bob Hanson: uploaded a new version of "Image:Nature10954 fig1c.spt"

Sandbox Reserved 1431

2018-01-30T02:31:35Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

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.

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure by dragging it around using your mouse or clicking the buttons below. Press SHIFT to zoom.

<jmol><jmollink><text>(a) exocellular view</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) endocellular</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) trans-membrane view</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) trans-membrane view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-30T02:29:19Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

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.

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure by dragging it around using your mouse or clicking the buttons below. Press SHIFT to zoom.

<jmol><jmollink><text>(a) Top view</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(b) Bottom view</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(c) Side view</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(d) Side view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/f/fc/Nature10954_fig1c.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

Sandbox Reserved 1431

2018-01-30T02:26:49Z

Bob Hanson: /* Crystal structure of the µ-opioid receptor bound to a morphinan antagonist */

==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==

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.

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
doi:10.1038/nature10954]

<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
'''Figure 1: Overall view of the µ-OR structure'''
Shown in <jmol><jmollink><text>Figure 1</text><script>exit;figure="http://proteopedia.org/wiki/images/2/20/Nature10954Fig1aLeft_4dkl-2.png";SCRIPT @figure</script></jmollink></jmol> is an overall view of the µ-opioid receptor bound to the morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]). The seven parallel trans-membrane helices are the signature of a "TM7" cell membrane receptor, spanning the 35-40 nm distance across the lipid bilayer of the cell.

At the top we see three extracellular loops, EC1, EC2, and EC3. Below, we see a short helix that is inside the cell.

Notice that the inhibitor, shown as space-filling spheres, is nestled relatively deeply within the helical core. Binding at this position effects a change in conformation through a twisting action of the helices. This twisting gets delivered to a second binding site of the receptor. This second binding site is attached to the helical assembly via TM3 and TM6 (not shown here). It is where an associated protein that binds GTP can bind. This protein's binding is what makes this receptor a "G-protein-coupled receptor." Its binding triggers the transmission of the chemical "signal" delivered by the opioid (or, in this case, being prevented from doing that).

Investigate the structure by dragging it around using your mouse or clicking the buttons below. Press SHIFT to zoom.

<jmol><jmollink><text>(a) Side view</text><script>SCRIPT http://proteopedia.org/wiki/images/c/ca/Nature10954_fig1c.spt('side')</script></jmollink></jmol>

<jmol><jmollink><text>(b) Top view</text><script>SCRIPT http://proteopedia.org/wiki/images/c/ca/Nature10954_fig1c.spt('top')</script></jmollink></jmol>

<jmol><jmollink><text>(c) Bottom view</text><script>SCRIPT http://proteopedia.org/wiki/images/c/ca/Nature10954_fig1c.spt('bottom')</script></jmollink></jmol>

<jmol><jmollink><text>(d) Side view with abstract membrane</text><script>SCRIPT http://proteopedia.org/wiki/images/c/ca/Nature10954_fig1c.spt('draw')</script></jmollink></jmol>

</StructureSection>

<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>

/wiki/images/8/8b/4dkl-local-contact.png
code for the above (space inserted just after the : <code><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>

is a close-up view of a bound to the µ-opioid receptor. The green circles indicate hydrogen bonds. <references/>

File:Nature10954 fig1c.spt

2018-01-30T02:26:07Z

Bob Hanson:

File:Nature10954 fig1b.spt

2018-01-30T02:25:04Z

Bob Hanson: uploaded a new version of "Image:Nature10954 fig1b.spt"

Figure 1 scripts

File:Nature10954 fig1b.spt

2018-01-30T02:24:36Z

Bob Hanson: uploaded a new version of "Image:Nature10954 fig1b.spt"

Figure 1 scripts

File:Nature10954 fig1b.spt

2018-01-30T02:23:08Z

Bob Hanson: uploaded a new version of "Image:Nature10954 fig1b.spt": Figure 1 scripts

Figure 1 scripts

File:Nature10954 fig1b.spt

2018-01-30T02:22:12Z

Bob Hanson: uploaded a new version of "Image:Nature10954 fig1b.spt": Figure 1 scripts

Figure 1 scripts