|
|
|
|
||
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.
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 unitsWhen 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. |
||
|
©2007 RCSB PDB |