wwPDB: Searching for structure information

In this chapter, we will explore different web interfaces for searching the archive of experimental protein structures and learn about their advantages.

The wwPDB is the single world-wide organization archiving experimental macromolecular structures. The archive currently holds over 100000 structures (updated number) and spans experimental data sources from Xray crystallography (XRAY), Nuclear Magnetic Resonance (NMR) or Electron Microscopy (EM). For a full list please see this link.

The rcsb.org web site is one of three main interfaces to the wwPDB archive. It features a very intuitive data presentation, that allows searching by simple text/keyword and features complex advanced queries as well. Please familiarize yourself with the summary page of 1AKE (please enter "1AKE" into the search field near the top of the screen).

Consider the panel describing experimental details of the deposition "1AKE", an adenylate kinase. Note that the resolution was determined to be 2.00 Å. Along with the space group the unit cell dimensions are given.

Now let us turn to the summary panel "molecular description". Please note that the details specified here consider the species the protein originated from along with gene names and if possible the protein's function. More detailed information is given in the graphical depiction "Protein Feature View".

The next panel of interest concerns structure validation. It is important to remind ourselves that checking the quality of any data we work with is crucial for determining its utility. Please inspect the Ramachandran plot for outliers.

Last let us inspect the ligand panel. Here the ligand with the three letter Code A5P is listed. Can you imagine why this ligand is present and why it is not possible to observe the natural substrate?