Welcome to PDBeXplore – the PDB browser!

PDBe proudly presents: PDBeXplore – a browser of structural knowledge

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 is now launching a new tool (called PDBeXplore) 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:

the Enzyme Classification (EC) system; pdbe.org/ec
the sequence-based protein-family classification system Pfam; pdbe.org/pfam
the fold-based protein-family classification system CATH; pdbe.org/cath
the compounds in the PDB; pdbe.org/compounds
the taxonomy classification system; pdbe.org/taxonomy
the gene ontologies in the PDB; pdbe.org/go

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).

How can I use the enzyme browser?

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:

start typing a name or number of an enzyme in the input box. Once you have typed a few characters, a drop-down menu will list the matches in the EC system – you can then select the appropriate one and hit the “Submit” button.

click on a class in the EC hierarchy below the input box. The class will be expanded to reveal all its subclasses. Note how all PDB entries containing enzymes of that EC class are loaded in the central panel and how the right-hand panel displays information about the EC class and the number of entries for it in the PDB. Continue expanding the EC tree until you have found the class you are interested in.

In this example, we will look at glutathione transferases (EC class 2.5.1.18).

How can I analyse the PDB entries for my enzyme class?

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.

Surely there is more?

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.

The “Ligands” tab shows you all heterogenic compounds that occur in the selected PDB entries, sorted initially by the number of entries they occur in. This usually reveals what co-factors, metals, etc. members of the selected enzyme class commonly bind. If you invert the sort order, you will find ligands that occur only once or twice – these may include compounds that act as inhibitors, substrate analogues, etc. In the case of glutathione transferase, the protonated and deprotonated forms of glutathione are in the top (not surprisingly). Why is “MES” such a commonly found ligand?

The “Structure folds” tab reveals the various folds, as defined by CATH, observed in the selected PDB entries (note that not all proteins contained in these entries necessarily belong to the selected EC class, so this can also give you clues about the folds of proteins that form complexes with these enzymes). Two pie charts show the distributions of commonly occurring CATH Class and Architecture types, respectively. Why is there a roughly 50:50 split between mainly-alpha and alpha/beta folds for the glutathione transferases?

The “Assemblies” tab looks similar to the previous tab, but instead shows information about the observed quaternary structures in the selected PDB files. In this case, for instance, it reveals that >90% of the assemblies are homomeric and >95% of these are dimers. If you know your glutathione transferases these numbers come as no surprise, but if you analyse a family of enzymes you are less familiar with, the analysis can be very informative.

The “Sequence families” tab provides a table with all the Pfam families observed in the selected PDB entries.

The “Organisms” tab provides information about the taxonomic classification of the source organisms of the selected PDB entries.

The “Publications” tab lists all published papers describing one or more of the selected PDB entries.

The “Links” tab provides cross-references (if available) to some other resources, including CAS, GO, ProSite and UniProt.

The “Authors” tab shows which structural biologists have determined the selected structures. The author names are sorted initially by the number of entries they have (co-)authored. This is a very useful tool to find out who is active in a certain field (for instance, if you are looking for collaborators, referees, or people who can give you crystallisation tips).

More browsers

This was a brief introduction to the enzyme-structure browser. You should now be able to explore the other browser modules yourself:

the Pfam browser – pdbe.org/pfam (for instance, explore the DEAD/DEAH box helicases, Pfam family PF00270)
the CATH browser – pdbe.org/cath (for instance, explore the orthogonal alpha-helical bundle fold, CATH architecture 1.1)
the Compounds browser – pdbe.org/compounds (for instance, explore the Adenosine-5'-Triphosphate using the three letters code ATP)
the Taxonomy browser – pdbe.org/taxonomy (for instance, explore all "Homo Sapiens" protein structures in the PDB)
the GO browser – pdbe.org/go - (for instance, explore the "GO:0008144 - drug binding" GO term)
the sequence-search browser – pdbe.org/fasta - if you don’t have a one-letter sequence handy, try this one:

TMCYSHTTTS RAILTNCGEN SCYRKSRRHP PKMVLGRGCG CPPGDDNLEV KCCTSPDKCN Y

Feedback

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.