The September 03, 2013 release offers:
New tool to search for drugs and drug targets in the PDB
Improved interface for 3D visualization using Jmol
Visualize, browse, and search protein symmetry and stoichiometry
Customized sequence identity cutoffs for sequence searches
Find Drugs in the PDB. Two new tables provide access to drug and drug target information from DrugBank that are mapped to PDB entries with each weekly update. These tables, accessed from the Tools menu, can be searched by generic or brand drug name, filtered, and sorted.
The Drugs Bound to Primary Targets Table lists drugs bound to primary target(s), or a homolog of primary target(s), i.e., co-crystal structures of drugs.
The Primary Drug Targets Table lists primary drug targets in the PDB, regardless if the drug molecule is part of the PDB entry (e.g., apo forms of drug targets, drug target with different bound ligands). Biotherapeutics, such as complexes with monoclonal antibodies, are included.
A detailed description of the Drug and Drug Target Mapping page is available.
The 3D View page has been redesigned to provide easy access to Jmol features.
A help page for this 3D View/Jmol page is available.
Users can now access the 3D View page through a new tab simply called "3D View", located right next to the
summary tab on the structure summary page.
Four Distinct Display Modes. Select from four modes of predefined style and color settings for Jmol.
The default mode colors residues by 'Secondary Structure'. The 'Subunit' mode renders all protein subunits in different colors,
and the 'Symmetry' mode emphasizes the point group symmetry or helical symmetry of a protein complex. The custom view can be used to access
additional options for style, color, surface rendering, and more.
View Hemoglobin 4HHB in different display modes:
View Secondary Structure
Analyze Protein Symmetry in the PDB.
The following symmetries are observed in protein quaternary structure. The new features
described below show how to visualize, search, and browse for symmetry and composition (stoichiometry) of protein subunits.
Legend: (Left to Right) PDB ID 3EAM: global C5 symmetry;
PDB ID 1LTI: local C5 symmetry ;
PDB ID 1IFD: helical symmetry.
Visualize Protein Symmetry.
View the symmetry of a protein complex. The Symmetry Display mode on the Jmol page highlights the symmetry relationships
among subunits by displaying symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.
The previous website release included only global symmetry.
This release includes two new symmetry visualization features: (1) local and (2) helical symmetry.
For local symmetry, the symmetric parts of the structure are displayed in color and the asymmetric parts are displayed in grayscale.
For helical structures, we display a helix axis and color the subunits in spectral color scheme.
Read more about how to visualize symmetry.
Explore Symmetry in the PDB.
From the Explore Archive widget on the home page or any query results page, drill-down by Protein Symmetry and Protein
Stoichiometry or any other classification to find a subset of proteins of interest.
For this release, asymmetric protein structures have been removed from the cylic drilldown, and moved into
its own drilldown. A new drilldown for helical structures has been added.
Search for Symmetry and Stoichiometry.
Search for a specific protein symmetry or protein stoichiometry and combine
these searches with any other advanced searches using AND or OR conjunctions.
Try out the Protein Symmetry Advanced Search for Point Group C5
Global Symmetry and Pseudosymmetry. The Browse Protein Symmetry tool provides access to more advanced symmetry
types such as global and local symmetry, and pseudosymmetry for homologous protein subunits.
Read more about how to browse for Protein Symmetry
Try out the Protein Symmetry browser
Sequence Identity Cutoff. A sequence identity cutoff value option was added to Advanced Search for sequence searches.
The sequence identity cutoff value is used in the sequence search to return results that have at least the specified sequence identity to the target sequence.
The RCSB PDB (
citation ) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.