User:Karsten Theis/overall views

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Introduction

This is a collection of how entire protein structures are depicted in publications. The most common views show

  • fold of domains
  • charge distribution
  • hydrophobic patches
  • surface conservation
  • superpositions with related structures

Standard and other views

In publications where figures are two dimensional and non-interactive, researchers have to choose a view that shows as much of the interesting features of the protein as possible. Often, when that is not possible, there will be two orthoganal views (e.g. the second rotated by 90 or 180 degrees. The protein used as an example here is the DNA repair enzyme UvrB in complex with ATP (PDB ID 1d9z). This protein not only binds to ATP, but also to DNA and to another DNA repair protein, UvrA. As you look at the various ways protein structures are depicted, you can zoom in to the different binding surfaces or zoom out to the standard view showing the entire protein with the "business" side facing you.




Types of overall views

Automatically generated figure for UvrB structure, PDBID 1d9z

References

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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