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1 BUILDING A STRUCTURAL MODEL OF KCSA 6

1 Building a Structural Model of KcsA

In this unit you will build the KcsA tetramer solvated in water, learning how to

take a raw protein structure and build a simulation-ready system out of it.

1.1 Downloading and Viewing the Protein

Our ﬁrst step is to download the raw protein structure from the Protein Data

Bank, an online repository for protein structures experimentally resolved, and

view it using VMD. The PDB ﬁle 1K4C.pdb contains the atom coordinates of a

monomer of KcsA.

1 Open a web browser and navigate to www.pdb.org. The ﬁle we will down-

load is also provided in mem-tutorial-files/01-BUILD/example-output/.

2 In the search box at the top center, select PDB ID or keyword, then type

1K4C and click Site Search. Each PDB ﬁle in the database has a unique

code of four letters or numbers identifying it. One may also search using

the name of one of the publishing authors.

3 On the left-hand side, click Download Files below 1K4C, then click PDB

text. You will be prompted to save the ﬁle 1K4C.pdb, which you should

place in mem-tutorial-files/01-BUILD/.

From now on, in this unit we will work with ﬁles located at

mem-tutorial-files/01-BUILD. Use the cd command in a terminal window

(or in VMD’s Tk Console when applicable) to set the correct directory.

4 Now close the web browser, open VMD, and load the ﬁle 1K4C.pdb that

you just saved.

5 This ﬁle contains not only a monomer of the KcsA protein, but also ev-

erything else solved from the c rystal structure. Set up the following rep-

resentations to see this:

Selection Drawing Method Coloring Method

protein NewCartoon Chain

not protein VDW Name

We see that the PDB ﬁle also contains water molecules, ions, large an-

tibody complexes (used to crystallize the KcsA) as well as some lipid

fragments (Fig. 2). These diﬀerent structural elements are divided into

“chains” in the PDB ﬁle, which we will see in detail in the next section.

For now, the point is simply that the PDB ﬁles you download will contain

structures that you want and structures that you don’t, but that these are

easily separated from one another.

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