This web page was produced as an assignment for an undergraduate course at Davidson College.

3D Structure of OmpF Porin

CPK Color Scheme

Exploring the OmpF Porin Structure

*Note to all viewers. For optimal viewing pleasure, please view Chime buttons in order from top to bottom. I would recommend going through the entire button list first without touching the image display so that you may view exactly what each button says. Otherwise, you may get a view other than what is meant to be shown.

1) Reset the view of OmpF porin. Click here.

2) Take a quick look at the entire protein through the eyes of a small polar molecule. Click here.

3) View the secondary structure cartoon. Click here.

Beta strands: Yellow

Alpha strands: Pink

Inside the Protein

4) The channel of OmpF porin is constricted by an internal loop dubbed L3. Click here to view L3. Click the button a second time to highlight L3.

L3 is lined with basic and acidic residues on opposing sides that provide the charge gradient needed for OmpF porin to inhibit large nonpolar substances from entering the cell. Here is a closer look at these residues:

The Basic Residues-

5) Shown is the positively charged Arginine 42 (ARG42). View here .

6) Next to ARG42 is the positively charged Arginine 82 (ARG82). View here.

7) Next to ARG82 is the positively charged Arginine 132 (ARG132). View here.

The Acidic Residues-

8) Shown is the negatively charged Aspartic acid 113 (ASP113). View here.

9) Next to ASP113 is the negatively charged Glutamic acid 117 (GLU117). View here.

10) Click here to view these amino acids on L3.

11) While the monomer of OmpF porin is shown at the left, the protein is commonly found in a trimer pattern. A "latching" loop, L2, is what connects one monomer to the other two. View loop L2 here.

12) Aspartic acid 74 (ASP74), one of the amino acids located on L2, can be identified here.

13) Reset the view of OmpF porin. Click here.

*Feel free to play around with this molecule's options by using the mouse to right-click the image for Windows users. For MAC users, click and hold over the image with the left-most button of the mouse.


Phale S, Philippsen A, Widmer C, Phale V, Rosenbusch J, Schirmer T. 2001 May. Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation. Biochemistry 40 (21): 6319-6325. <>. Accessed 2005 Feb 15.


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