User:Craig T Martin/Sandbox 1

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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.

Examining the , we see that there is structured peptide reaching out from the protein (on the left, in the unrotated view). There is no reason that this element should have structure (no hydrophobic core to stabilize).� Yet it is observed as structured in the PDB data. Why?

Whenever you see something like this, the likely answer is crystal contacts: this peptide is interacting with a neighboring molecule in the crystal. We can use the following command in Pymol to generate neighboring molecules in the crystal.

Generate only those within 5.0 angstroms of our protein:

symexp sym, 1jy1,(1jy1),5

Generate only those within 4.5 angstroms of the selection:

symexp sym, 1jy1,(sele),4.5

Using the first command, I generated all of those in contact, but then turned off the ones not contacting this part of my protein (there ARE contacts also with other parts of the protein!), to see . You can see that the green protein interacts with the red element we saw before, and then in turn, the red protein is stabilizing the same element in the blue protein, etc.

I then generated a surface view in Pymol, to illustrate that . That's why it has structure in the crystal. In solution, however, that neighbor protein is likely not there, and that extended peptide either docks back onto its parent protein or is unstructured.

Function

Disease

Relevance

Structural highlights

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. Now try it with .