Protein DataBase (PDB) Viewing

Discovery Questions

PDB requires Chime Plug-in. Mac users must use Netscape.

Part One

1) Go to this <> and enter this file "1dxx". This file only contains the amino portion of the full dystrophin protein. View this fragment using the "QuickPDB" method (this file is a homotetramer).

2) Within this window, find this sequence DVQKKTFTKW and highlight it (it begins at amino acid 15). What kind of secondary structure does it help form?

Part One

1) Go to this <> and enter this file "1ai3" View the structure using "Protein Explorer".

2) Make sure your window is properly sized and then click on the button to view 1AI3 from the PDB server. Although it takes a while to load, do not do anything until you see a spinning model of IDH.

3) In the upper right frame, you will see a link that says “Explore 1AI3”. Click on this and wait until you see a green box that says ready appear below the structure of IDH.

4) A new set of buttons will appear in the top right frame. Click once on the one that says “water” and most of the red balls will turn to spheres of dots. Click again and they disappear.

5) Click on the other buttons to see what happens.

Part Three

For advanced users: Try to compare two structures in Protein Explorer. You can try fragments from: the human prion protein (1fkc) the bovin prion protein (1dxo) or the yeast prion protein Ure2 (1g6w)

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