What's in a PDB file?

Each structure is submitted to the Protein Data Bank as a computer file with a specific format. This file contains information about the structure such as:

• name of the molecule
• the organism it comes from
• date the structure was submitted
• reference to scientific papers about this structure
• the method used to determine the structure
• crystallographic resolution, where approproiate
• the (amino acid) sequence
• ligands bound
• important residues, such as active sites
• 3 dimensional coordinates of all the atoms involved

Some of this information is extracted within the Protein Data Bank and/or PDBsum, and you can view it on the relevant web pages, as we saw last week, but it is also useful to know where this can be found within the Protein Data Bank file itself.

To look at what is in a PDB file, go to the Protein Data Bank website. Search for the structure with code 1TPH. Download the file corresponding to this structure and open using WordPad.

There is quite a lot of educational information on the Protein Data Bank website itself.

Use the information in this PDB file to answer the questions.