Vitamin D 25- Hydroxylase

Vitamin D 25- Hydroxylase is an enzyme involved in the cascade of reactions responsible for converting Vit. D into an active human form. This protein is a dimer with two surface and two interior active sites. Our picture highlights the two oxygen ring active sites (RED) in there respective domains. The oxygen rings bind to the heme iron groups (Royal Blue) which mediate electron transfer, critical for activating the Vitamin D. Vitamin D Hydroxylase

By Nicholas Lopes, Craig Conner, Lonnie Yu


This innocuous looking protein is the “Crystal structure of Reston Ebola VP35 interferon inhibitory domain“.  It’s accession code on the protein data bank is 3L2A.  The red spirals are alpha helices and the yellow portion is a beta sheet.  The green sections aren’t part of a set structure, and the tiny ‘starry’ flecks are incorporated water molecules.  This is a ‘cartoon’ format to allow for closer observation of structures within the viral protein.  So sayeth Will Jordan


Since I lived in Toronto during the Sars outbreak I decided it to use it as my protein. Sars stands for Severe acute respiratory syndrome and it is a Papain-Like Protease Inhibitors.


In this image I show where the ligand binding site is for the protein and by using mesh view it allows us to see the pocket in which the ligand binds. Red are helices, Yellow are beta sheets and green are loops. The green spheres are the ligand.

Sars binding site

Sars binding site

Green Flourescent Protein (GFP)

Below are two images of Green Fluorescent Protein, which was originally found in a species of  cold-water jellyfish and is now an essential tool for scientists and ravers alike.  It absorbs UV light and re-emits it as green.  It appears to be composed of two beta-sheet tubes, (red) which are rotated slightly with respect to each other and are not attached by any sort of molecular chain.  There is some alpha helix (blue) on the inside of the tubes; surely, this is also important.

The protein is shown as a cartoon (left) and with a surface mesh (right).

For all of this information and more, see:

heptameric SAP-like pentraxin (a.k.a. The Cheerio)

Jonathan, Stephanie, and Austin discovered this protein (known as “The Cheerio”) in mid summer 2010 during the Skills for Success Workshop. This protein (3FLP) made of two stacked cyclic molecular aggregations (CMA), with each CMA having either 7 or 8 domains, depending on the organism in which it is found. 3FLP is classified as a sugar binding protein and is an important effector protein of the hemolymph immune system.

This animated GIF was created using PyMol’s Save Movie As > Image and GIFFun. The spectrum of colors was used to help distinguish the individual domains of the protein. Using a surface makes it easier to view the protein as a cheerio.


We Love Caffeine

Caffeine is obviously a great drug.  It’s formula is C8H10N4O2 and is classified as a hydrolase.  It’s structural weight is 44434.5 and it’s lentgh 406 Angstrom.

It also is pretty looking and might make a nice wallpaper.  To create this picture we used the “Cartoon feature” in rainbox color and made the background white.  We then added in the”sticks” so the picture looked fuller.  We also have consumed 6 cups of coffee this morning in preparation for this task.pretty caffeine

This post was created by Sara K., Timkhrit B., and Pelagie F..

Pymol Protein Picture

This is the Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA). Picture made in Pymol; helix is blue, sheet is red, and loop is pink.


Anthrax (1jky) and Calponin (3I6X) by Denise Koessler


The first picture here is one of three sections of Anthrax.  In anthrax toxin, there are three molecules: a delivery molecule while delivers the other two parts: edema factor and lethal factor.  The cartoon protein fold below is of the Lethal Factor of Anthrax Toxin.  (clearly the most important)  If  you are interested in more information about this protein, go here.

The Lethal Part of Anthrax


This is the “Cartoon” version of 3I6X Calponin. I selected this picture for my post because I enjoyed the coloring of the alpha helices.   In this view, I wanted to show the two main domains of this structure, so this protein is potentially a ‘dimer.’  Maybe… according to my biology friends…

My Protein_3I6X_calponin

Here are some factiods about this protein from the RCSB Protein Data Bank:

Structure Weight: 89550.40
Molecule: Ras GTPase-activating-like protein IQGAP1
Polymer: 1 Type: polypeptide(L) Length: 193
Chains: A, B, C, D
Fragment: N terminal calponin homology domain (UNP residues 1-191)


Figure 1. N-terminal domain of carcinoembryonic antigen-related cell adhesion molecule 5

Figure 1. N-terminal domain of carcinoembryonic antigen-related cell adhesion molecule 5. Beta-sheets are colored yellow, alpha-helices are colored red.


prettttttttttyprotein picture2

This is CHK1 Checkpoint Kinase. I made the picture in Pymol.