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a. Thumbnail image(s)  b. Contents f. Enzyme reaction		c. Header details d. Links e. Molecular surface and clefts
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a. Thumbnail image(s)

Main view	Bottom view	Right view

The thumbnail image(s) are rendered using Raster3D and show the complete structure in the given entry. Depending on the structure, either one or three views are shown; the latter are for structures containing DNA/RNA molecules (as in the example above) or ones containing elongated proteins/multimers. The three orthogonal views - main view, side view and bottom view - are intended to give a better idea of the 3D structure in those cases where a single view can be misleading. The main view always corresponds to the orientation defined by the coordinates deposited with the PDB.

Proteins are depicted in terms of their secondary structure: cylinders correspond to helices, arrows to beta strands and threads to random coil. The colour of each protein chain is determined by its chain identifier, the colours (purple, red, brown, pink, blue, green, cyan and yellow) being assigned to different chains as follows:

Ligands and metals are shown in spacefill. DNA and RNA chains are depicted by thick bonds with the backbone trace coloured according to the chain identifier, as above.

b. Contents

1 2 3 4 5 6 7 8		1. On many entries the small silhouette above the thumbnail image of the structure represents the species from which the protein/DNA comes (here the species represented is one called Homo sapiens). Clicking on the picture takes you to a list of all other PDB entries from the same species. A full analysis of entries by species can be found here. 2. The thumbnail image has already been described above. 3. The icons below the thumbnail image do the following:   MolScript/Raster3D. Takes you to a page where you can generate a MolScript or Raster3D plot of the structure (or of selected chains from it). Instructions are provided on the page in question.   RasMol. If your browser has been correctly configured (see below) clicking on this icon loads the structure into the RasMol molecular graphics program, rendered as in the thumbnail image.   Help on RasMol. Instructions on downloading RasMol and configuring your browser so that it automatically displays the relevant molecular graphics image when you click on the RasMol icon. The instructions can also be found here.   PROCHECK. Provides a Ramachandran plot for all protein residues in the structure, together with summary measures of the stereochemical quality of the protein chains, as generated by the PROCHECK program. 4. Header details. The header details (selected by default) are shown on the right of the page and described at c. Header details below. 5. Header records. Clicking on this link will show the header records from the original PDB file. 6. Protein chain(s). The protein chains in the structure are listed here, together with their sequence lengths (in terms of number of amino acid residues). Clicking on the link takes you to a summary of the protein's secondary structure motifs and "wiring diagram" (as described under the Protein tab above). Identical, or very highly similar, chains are grouped together and only described once. 7. DNA/RNA, ligands and metal ions. Any other molecules in the structure are listed here and analysed on further pages accessed by clicking on their links. 8. Go to PDB code. This box allows you to enter any other PDB code and jump directly to its PDBsum page.

c. Header details

The Header details on the right hand side of the page provide information largely taken from the PDB header record. The details include the name, date and description of the macromolecule(s) in the entry, its authors, resolution and R-factor(s).

For enzymes, the Enzyme Classification (E.C.) number is given, together with links to several enzyme databases. The enzyme reaction the protein catalyses is also shown and, in some cases a diagram depicting the reaction appears at the bottom of the page (described under f. Enzyme reaction below). As the enzyme classification is frequently incorrect in the PDB files, the information used in PDBsum comes from the PDBe database.

If an entry has been superseded, a link is given to the newer release of the structure. Conversely, links are given from the newer structures to the entries they supersede.

d. Links

e. Molecular surface and clefts

For molecules that are not too large, the molecular surface and clets in that surface are computed and can be viewed in RasMol. The top ten largest clefts in the surface are shown coloured in decreasing volume: red, purple, yellow, blue, green, brown, pink, greenblue, magenta, cyan.

f. Enzyme reaction

For some enzymes the molecules involved in the reaction catalysed by the enzyme are shown. The molecular diagrams are generated from .mol files obtained from the KEGG ftp site.