Instructions
for Completing sub-part 7 (or G)
of problem one on the Internet special assignment:

You won't be able to answer the last sub-part of question 1 simply by looking at the webpage associated with the PDB entry. Instead, you will need to actually examine the PDB structure file, which you can download by clicking on "Download Files", near the upper right-hand corner of the structure's webpage. One of the entries will say "PDB Format"; click that and open the resulting downloaded file with a text-file reader or a word-processing program.

There are at least two ways to count the number of solvent molecules in the structure, once you're looking at that text file: one is to actually count the number of water and non-water solvent molecule records found within the file. The other is to look within the file for a line that says something like
FORMUL 3 HOH *103(H2 O)
which means that there are 103 records containing information about water molecules. If there are solvent molecules other than water in your structure, there will be FORMUL lines describing those as well; you'll have to do a bit of counting to total all that up.

What I've asked for, though, is the number of solvent molecules per protein monomer, so to get that number, you'll need to divide the total number of solvent molecules by the number of protein monomers in the structure. That you can figure out directly from the structure's PDB webpage: under "Macromolecules" it shows you the names of all the macromolecular "Chains" found in the reported structure. If there are three macromolecular chains (often labeled A, B, and C), and you've found 380 water molecules and 10 non-wateer solvent molecules by the previous instruction, then the number of solvent molecules per chain is (380+10)/3 = 390/3 = 130.

If you have other questions about completing this assignment, ask me. I promise to answer promptly.