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
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
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
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.
Introduction to Biological Units and the
PDB Archive is available to describe asymmetric and biological
units in more detail.
biological unit of 1AEW.
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
Unique # visits
293105 503.15 GB
300115 504.13 GB
258107 424.74 GB