Exploring Ligands in the RCSB PDB Database

A ligand name can be entered in the keyword text search at the top of any page from the RCSB PDB website. The Advanced Search query engine can also be used to search for structures based upon ligands -- based upon the ligand's name, ID code, or SMILES string.

In addition to reviewing the structures that match the given query constraints, users can select the 'Ligand Hits' tab, which lists the ligands known to interact with the structures matching the query.

  The Ligand Hits tab also offers a gallery view of ligand images.

Selecting one of the ligands from this tab returns a summary page with chemical and structural details. The page offers interactive and static views of the ligand. Users may also download 'model' coordinates (the experimental coordinates from the first deposition of the ligand) and 'ideal coordinates' (generated from the model coordinates and their connectivity) in a variety of formats including CIF, XML, SDF and PDB.


Using Simple Viewer to visualize functional biological units

(Click image to enlarge)
The biological unit of 1AEW in Simple Viewer

When crystallographic structures are deposited in the PDB, the primary coordinate file generally contains one asymmetric unit - a concept that has applicability only to crystallography. For many of these structures, the asymmetric unit represents the functional biological molecule. In other cases, the biological unit can be generated from the asymmetric unit.

In these cases, Protein Workshop can be used to display the asymmetric unit and Simple Viewer can be used to explore the functional biological unit of a structure. Simple Viewer can rotate a structure, zoom in and out, and then save the view of the biological unit as an image file.

Simple Viewer tool can be launched from the "Display Options" found on an entry's Structure Summary page. Simple Viewer requires Java version 1.4 or greater.

Citation information is available for images created using Simple Viewer.

An Introduction to Biological Units and the PDB Archive is available to describe asymmetric and biological units in more detail.

The biological unit of 1AEW.

The asymmetric unit of 1AEW.



Using PubMed Abstracts to Search the PDB

PubMed abstracts are accessible from a published entry's Structure Summary page. The "Abstract" link returns a page with the article title, abstract, keywords, authors, organizational affiliation, journal, and PubMed identifier. The PubMed abstract at NCBI can also be viewed by clicking on the icon next to "Abstract".

The text box at the bottom of the Abstract page can be used to search for related structures in the PDB using any word in the abstract or keyword fields. Terms can be entered into the text box either by typing the word manually or by clicking the mouse over any word in the abstract or the keyword fields.




Access statistics for the first quarter of 2007 are given below for the RCSB PDB website at

Month        Unique    # visits        Bandwidth

Apr 2007    122991    293105        503.15 GB

May 2007    123069    300115        504.13 GB

Jun 2007    104693    258107        424.74 GB