Posts Tagged Structural Biology

Fun with Pymol

The combination of PDB and Pymol creates a great tool to visualize protein structures and manipulate them. The structure above is Aldo-Keto Reductase, which is a stress enzyme found in plants. In this view, you can see NADP bound to it in blue, with alpha helices in red and beta sheets in yellow.

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P53 Protein (Ben/Kyle)

This is a well known Tumor Suppressor protein. 3 are shown below near a DNA molecule.

Here is a consurf image of the same protein. (darker areas are more conserved)

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Protein visualization (Rachel / Thomas)

Solved crystal structure of BRCA1 BRCT (made in Jmol):

Electrostatic map of BRCA1 BRCT (made in Pymol):

Sequence of BRCA1 BRCT showing features such as beta strands and alpha helices:

The structure has a diameter of ~27 A.  ~55 A in length.

There are a variety of secondary structures including beta turns, beta strands and alpha helices.

BRCA1 is composed of 215 residues.

Conserf run (MSA):

Dark purple regions are conserved.  Notice ligands binding in that region.

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