Traditionally, the Protein Data Bank (PDB) has been accessed mostly by PDB accession code, or by searches based on information regarding, for instance, a publication, a molecule name, a sequence or a related 3D structure. While these methods are valuable for locating a specific PDB entry or group of entries, they are limited in their application and the result of such searches is usually a list of PDB entries and some of their attributes.
The Protein Data Bank in Europe (PDBe; pdbe.org) has traditionally distinguished itself from similar resources by providing advanced services built on the structural data contained in the PDB, such as a fold-recognition and structural alignment server (SSM or PDBeFold; pdbe.org/pdbefold), a tool for analysis of sequence, structure and function based on 3D motifs (PDBeMotif; pdbe.org/pdbemotif) and a tool for analysis of the quaternary structure of biomacromolecular assemblies (PDBePISA; pdbe.org/pdbepisa).
Continuing this tradition of providing advanced and innovative services, PDBe has developed PDBeXplore, a tool that can be used to browse, list and analyse the structural knowledge embodied in the PDB based on classification systems that are familiar and intuitive to molecular biologists, biochemists and other life scientists. At present, there are six browser modules that are based on:
In addition, PDBe offers a sequence-search facility of the proteins in the PDB whose results are also presented in the browser (pdbe.org/fasta).
The enzyme browser can be accessed at this URL: pdbe.org/ec
This browser provides an interface that enables you to retrieve and analyse information on any or all of the enzyme structures available in the PDB. The enzyme classification information is taken from the latest release of the IntEnz Enzyme database.
The browser consists of three components (discussed in more detail on the information page in the central panel when you first access the browser). The left-hand panel enables you to select those enzymes you are interested in, the right-hand panel displays information about the class of enzymes you have selected and the central panel presents a number of different views on the structural information available in the PDB about that enzyme class. All data is retrieved from the PDBe database in real time so that the information shown in tables and graphs is always up-to-date.
Browsing the structural archive in this fashion provides both expert and non-expert users with an intuitive method for accessing and analysing the wealth of information available in the PDB, using familiar biological or (bio-)chemical terminology and classifications.
There are two ways to make a selection of an enzyme class using the left-hand panel:
In this example, we will look at glutathione transferases (EC class 188.8.131.52).
In the previous section, it was explained how you can select a certain enzyme class and automatically retrieve all the entries in the PDB that contain one or more copies of an enzyme belonging to that class. In the example above, there were 237 hits, but this number will probably be different when you try it out yourself. This is because the browser uses the up-to-date structural database of PDBe.
The central panel shows a number of tabs (“PDB entries”, “Ligands”, etc.), each of which provides you with a different view or analysis of the selected PDB entries. The “PDB entries” tab is shown first and it contains a table with information of all the entries in the current release of the PDB that contain proteins belonging to the selected enzyme class.
The data can be sorted on any column by clicking on its header (clicking it a second time inverts the sort order). In the example above, the entries have been sorted on resolution, providing an immediate answer to the question: “What is the highest-resolution crystal structure of a glutathione transferase currently available in the PDB?”
If you mouse-over the PDB ID code you will see a miniature figure of the structure in that entry; a mouse-over on any of the ligand names will reveal the chemical formula of that ligand. Find out yourself where clicking on each of the links in a row of the table takes you.
If you would like to download the entire table as a text file, click on the link “Download table from central panel as text file (CSV)” in the right-hand panel at any time. This works in all the tabs that show a table. The sort order in the text file will be the same as that in the table when you saved the file.
If you only use the “PDB entries” tab, the browser does not provide much more information than a simple database search. More interesting information is presented in the other tabs of the central panel.
This was a brief introduction to the enzyme-structure browser. You should now be able to explore the other browser modules yourself:
We hope that the PDB browser will be useful for your work (as well as in teaching). We welcome your comments and suggestions – please use the "FEEDBACK" button at the top of this page.