Sandbox Reserved 1640

From Proteopedia

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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

Contents 1 Your Heading Here (maybe something like 'Structure') 2 Biological relevance and broader implications 3 Important amino acids 4 Structural highlights 5 Other important features 6 References

Your Heading Here (maybe something like 'Structure')

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image 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. Your Heading Here (maybe something like 'Structure and Function') spinqualitylabelsall models Ligand Binding sites of 6ZLk Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Function of your Protein The specific function of my protein is that it is an enzyme that comes from bacteria called Bacillus cereus. Its main function is to catalyze the chemical reaction by turning UDP-glucose into UDP- galactose in sugar-containing metabolites. It does this by flipping the chiral center. The PBD of this protein in 6ZLK and it contains 3 ligands. The 3 ligands are UGB, NAD, and UGA. I am focussing on is UGB.

Biological relevance and broader implications

Important amino acids

Structural highlights

Our protein comes from the Bacillus cereus HuA2-4 organism. It includes the Epimerase domain.  Our protein has a fair amount of secondary structures. I see that this protein possesses 12 helices and 12 beta-sheets. This tertiary structure contains many hydrophobic interactions. There are 3 major ligand binding sites.: UGA, NAD, and UGB. This means that the amino acids at the binding sites have nonpolar R groups cluster together, on the inside of the protein. This leaves the hydrophilic amino acids on the outside of the structure. This protein contains a few sugar rings in its metabolic pathway. The process creates sugar products. This enzyme creates a cavity where the sugar group binds and modifies itself. It has one Ramachandran Outlier. the total structure Weight is 153.40 kDa.The way that the protein is folded denotes that it might also be a quaternary structure.  

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.

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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

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