Being able to manipulate PDB files makes it easier to port your structure files from one application to another. This section presents a little primer on PDB file format, availability, and usage.

The best place to look is on the RCSB PDB database which has lots of structures. Some of there are crystallographic, some NMR based and some are theoretical. Also Nucleic Acids database for RNA and DNA structures although many of these are also in RCSB PDB.

For example here is a search for keywords “tyrosine kinase inhibitor” at Brookhaven [http://www.rcsb.org/pdb/results/results.do]. Notice, this returns a lush quantity of structures. One structure from this search is 2CM8.pdb and has a nice compliment of secondary structure, salt, and a bound ligand.

When you download structures from the PDB is worthwhile to look at the text of the PDB itself in your text editor to determine how many models there are and how they have been structured in the saved PDB document. You can use your text editor for this. In this case, this is a crystal structure with one model. The structure of the PDB is in old fortran so the positions of the columns actually matters. This is one of the reasons you may have had trouble porting your pdb into different applications.

breakdown of pdb cards and columns