Sandbox Reserved 1668
From Proteopedia
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{{Sandbox_Reserved_BHall_Sp21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{Sandbox_Reserved_BHall_Sp21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
| - | == | + | ==Structure of human PYCR1 complexed with THFA== |
<StructureSection load='6XOZ' size='340' side='right' caption='Caption for this structure' scene=''> | <StructureSection load='6XOZ' size='340' side='right' caption='Caption for this structure' scene=''> | ||
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
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== Function of your protein == | == 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. | 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 <scene name='87/873230/Protein_view_2/2'>black</scene>. | ||
== Biological relevance and broader implications == | == Biological relevance and broader implications == | ||
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== Important amino acids== | == Important amino acids== | ||
| - | Here is a <scene name='87/873230/Ligands/1'>ligands</scene> view, with all of the ligands visible. This is a <scene name='87/873230/Ligands_zoomed/1'>zoomed in</scene> 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. | + | Here is a <scene name='87/873230/Ligands/1'>ligands</scene> view, with all of the ligands visible. This is a <scene name='87/873230/Ligands_zoomed/1'>zoomed in</scene> 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. <scene name='87/873230/Amino_acid_view/1'>This view</scene> highlights all of those amino acids in magenta, with the protein transparency set to 90%. |
== Structural highlights == | == Structural highlights == | ||
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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. | 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 view of domain E's <scene name='87/873230/Tertiary_structure/2'>tertiary structure</scene>. | ||
| - | This is a <scene name='87/873230/Spacefill_view/ | + | This is a <scene name='87/873230/Spacefill_view/2'>space-filling</scene> view of 6XOZ. |
== Other important features == | == Other important features == | ||
| + | <scene name='87/873230/Hydrophobic_vs_polar/1'>This view</scene> shows us the hydrophobic areas in the protein in comparison with the polar areas. Looking <scene name='87/873230/Hydrophobic_vs_polar_closer/1'>closer</scene>, we can see that the ligands are located in hydrophobic areas. Proline is hydrophobic, meaning in order to bind, the binding site would need to be located in a hydrophobic region on the protein. In this <scene name='87/873230/Proline/1'>next image</scene>, you can see the locations of all the prolines. In <scene name='87/873230/Hydrophobic_vs_polar_vs_pro/1'>one more view</scene>, you can see the hydrophobic areas in grey, polar in pink, and proline in blue. This shows that prolines are located in the hydrophobic areas. | ||
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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. | ||
</StructureSection> | </StructureSection> | ||
Current revision
| 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. |
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Structure of human PYCR1 complexed with THFA
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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
