The most obvious change that has been made is to the appearance of the web pages. These have been modernized, simplified and structured in a more logical manner and are now generated dynamically. Each structure's home page now provides a thumbnail image(s) of the structure plus, below it, an index listing the molecules it contains, in terms of protein chain(s), DNA–RNA chains, small-molecule ligands, metal ions and number of water molecules. Clicking on the items in the index takes you to the analyses provided for that molecule type (secondary structure diagrams for protein chains, protein–ligand interactions for the ligands, and so on). The index thus provides an at-a-glance summary of the molecules contained in the PDB entry.
Much duplication of redundant information has been removed. Thus, for example, where a structure contains multiple copies of the same protein chain, only a representative chain is described in detail; previously all structures were rather unnecessarily described. This is reflected in the index, which groups together or separates the protein chains accordingly. So you can immediately see that, say, the structure consists of four chains (A, B, C and D) which are all equivalent, or conversely, that the structure consists of two dissimilar protein chains, A and B, etc. Similarly, for ligands, multiple copies of the same ligand, making identical interactions with equivalent protein chains, are now shown only once.
In addition to the thumbnail image and index of contents, the home page of each entry also provides the usual descriptive information (such as title, authors, date of deposition), links to other sequence and structure databases, summary PROCHECK (4
) analyses and a button for viewing the structure in RasMol (5
A novel feature is a link to a server that allows you to automatically generate your own image of the structure via MolScript (6
) and Raster3d (7
). Another new feature, for most enzyme structures, is a diagram of the reaction catalysed by the enzyme. The diagram shows chemical drawings of the reactants, products and, where relevant, cofactors. The drawings are generated from mol2 files that were downloaded from the KEGG (8
) ftp site. Of particular interest are structures where the bound ligand corresponds to, or is similar, to one of the molecules involved in the reaction. These are identified on the diagram with their percentage similarity to the molecule in question. Similarities are calculated by using a simple graph-match between the atom types and connectivities of the structure's ligands and the reaction molecules. Figure shows an example.
Figure 1 Diagram showing the reaction catalysed by enzymes of class E.C.22.214.171.124—the glucosamine 6-phosphate synthases. The diagram is taken from the PDBsum page for 1gdo, where the bound ligand—an l-glutamate—corresponds to one of the (more ...)