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Sandbox Reserved 1638

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{{Sandbox_Reserved_BHall_F20}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
{{Sandbox_Reserved_BHall_F20}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
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==Your Heading Here (maybe something like 'Structure')==
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==Structure==
<StructureSection load='6X0J' size='340' side='right' caption='Caption for this structure' scene=''>
<StructureSection load='6X0J' 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 &lt; and &gt; signs.
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
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== Function of your Protein ==
== Function of your Protein ==
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<scene name='86/861620/Regular_protein/1'>SidA catalyzes NADPH-dependent hydroxylation of ornithine through oxidative mechanisms.</scene>
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<scene name='86/861620/Regular_protein/1'>SidA catalyzes NADPH-dependent hydroxylation of ornithine through oxidative mechanisms.</scene> SidA acts as both a receptor and an enzyme. As a receptor it extracts metals such as iron and takes it into cells. It is also an enzyme because it uses the FAD in the reactions.
== Biological relevance and broader implications ==
== Biological relevance and broader implications ==
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<scene name='86/861620/Ligand_only/1'>Our structure has but also doesn't have ligands</scene>. The ligands it does have are NADPH and FAD and they're bound, just not to the substrate. There are 4 crystal structures formed. <scene name='86/861620/Secondary/1'>Our secondary structures are in orange and show the polypeptide chains in a helices.</scene> <scene name='86/861620/Cartoon/1'>You can see clearly the inside and outside of the protein.</scene> The outside green, pink, blue, and yellow show the beta sheets and helices in the secondary structure, about 90% helices and 10% beta. The important parts to recognize are the purple helices. <scene name='86/861620/Hydrophobic/1'>These are considered to be polar and hydrophobic.</scene>
<scene name='86/861620/Ligand_only/1'>Our structure has but also doesn't have ligands</scene>. The ligands it does have are NADPH and FAD and they're bound, just not to the substrate. There are 4 crystal structures formed. <scene name='86/861620/Secondary/1'>Our secondary structures are in orange and show the polypeptide chains in a helices.</scene> <scene name='86/861620/Cartoon/1'>You can see clearly the inside and outside of the protein.</scene> The outside green, pink, blue, and yellow show the beta sheets and helices in the secondary structure, about 90% helices and 10% beta. The important parts to recognize are the purple helices. <scene name='86/861620/Hydrophobic/1'>These are considered to be polar and hydrophobic.</scene>
== Other important features ==
== Other important features ==
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One feature is that <scene name='86/861620/Charge/1'>His is light blue and shows</scene> that the Pka is 6.0. The charges would either be red or blue and it doesn't look like those are present.
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One feature is that <scene name='86/861620/Charge/1'>His is light blue and shows</scene> that the Pka is 6.0. The charges would either be red or blue and it doesn't look like those are present. The other important feature is that there are <scene name='86/861620/Chains/1'>four separate chains</scene>. They are clearly marked by four separate colors and show different branches in the middle.
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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.
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</StructureSection>
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<ref>PMID:32723870</ref></StructureSection>
== References ==
== References ==
<references/>
<references/>

Current revision

This Sandbox is Reserved from 09/18/2020 through 03/20/2021 for use in CHEM 351 Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, IA. This reservation includes Sandbox Reserved 1628 through Sandbox Reserved 1642.
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

Caption for this structure

Drag the structure with the mouse to rotate

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ Campbell AC, Stiers KM, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics. J Biol Chem. 2020 Jul 28. pii: RA120.014750. doi: 10.1074/jbc.RA120.014750. PMID:32723870 doi:http://dx.doi.org/10.1074/jbc.RA120.014750
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