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Sandbox Reserved 1668

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Revision as of 23:46, 18 April 2021

This Sandbox is Reserved from 01/25/2021 through 04/30/2021 for use in Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1665 through Sandbox Reserved 1682.

To get started:

Click the edit this page tab at the top. Save the page after each step, then edit it again.
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

Structure of human PYCR1 complexed with THFA

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 ^[1] or to the article describing Jmol ^[2] to the rescue.

1 Function of your protein
2 Biological relevance and broader implications
3 Important amino acids
4 Structural highlights
5 Other important features

Function of your protein

PYCR1 is a protein involved in proline biosynthesis. THFA is a ligand that can bind to the active site on the PYCR1 protein. This inhibits PYCR1's ability to bind to proline-5-carboxylate to synthesize proline. Here is a view with the protein at 50% transparency and the ligands colored .

Biological relevance and broader implications

PYRC1 is the target for potential cancer therapy. THFA binds to the active site on the protein and inhibits it's ability to synthesize proline from proline-5-carboxylate. Cancer cells require more proline than a regular human cell, so finding a ligand to bind to the active site of PYCR1 and inhibit the synthesis of proline could potentially work to stop cancer cells growth and division. Unfortunately, THFA is not as good of an inhibitor than other ligands mentioned in the article, so further research is needed to find a better inhibitor.

Important amino acids

Here is a view, with all of the ligands visible. This is a picture of one of the THFA ligands on the PYCR1 protein. THFA interacts with the amino acids Serine 233, Valine 231, Threonine 238, and Alanine 237 from the PYCR1 protein. highlights all of those amino acids in magenta, with the protein transparency set to 90%.

Structural highlights

There are 5 domains. Among all of them, there is about 50% alpha helices, 40% beta sheets, and about 10% other structures. Alpha helices, beta sheets, and some of the other structures all are bonded to the different ligands. Some of the ligands bond to H2O “outside of the loop”. Here is a view of the highlighted in green, and this is a view of the highlighted in pink. This is a view of domain E's . This is a view of 6XOZ.

Other important features

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

^[1]

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1668"

@@ Line 19: / Line 19: @@
 Here is a view of the <scene name='87/873230/Alpha_helices/1'>alpha helices</scene> highlighted in green, and this is a view of the <scene name='87/873230/Beta_sheets/1'>beta sheets</scene> highlighted in pink.
 This is a view of domain E's <scene name='87/873230/Tertiary_structure/2'>tertiary structure</scene>.
-This is a <scene name='87/873230/Spacefill_view/1'>space-filling</scene> view of 6XOZ.
+This is a <scene name='87/873230/Spacefill_view/2'>space-filling</scene> view of 6XOZ.

Sandbox Reserved 1668

From Proteopedia

Revision as of 23:46, 18 April 2021

Structure of human PYCR1 complexed with THFA

Contents

Function of your protein

Biological relevance and broader implications

Important amino acids

Structural highlights

Other important features

References

Views

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