Protein Symmetry and StoichiometryThe calculation of protein symmetry and stoichiometry is one of the major features of this release. The goal is to better describe biological assemblies of proteins according to some of their characteristics.
Symmetry refers to the point group symmetry of a protein complex. Protein complexes with quaternary structure can have rotational symmetry belonging to the point groups: cyclic (Cn), dihedral (Dn), tetrahedral (T), octahedral (O), or icosahedral (I).
The stoichiometry of a protein complex represents the composition of its subunits. For example, the biological assembly of hemoglobin has two alpha and two beta subunits, represented by the formula A2B2.
Here a few examples:
The Crystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form
has a cyclic symmetry of C7 and is formed by a homo-7-mer (A7)
The Crystal structure of phosphoserine phosphatase from T. onnurineus has Dihedral - D4 symmetry and is formed by a homo-8-mer (A8)
Ferritin has Octahedral symmetry and is a Homo 24-mer
The Foot-and Mouth Disease Virus has Icosahedral symmetry and is formed by a Hetero-240 mer with the a A60B60C60D60 stoichiometry.
Tip: Enable the Axes and Polyhedron options on the Jmol page to get a better understanding of the composition of the protein.
Biologically Interesting Molecules
Various biologically interesting molecules, such as peptide-like antibiotic and inhibitor molecules are being annotated by the PDB. The latest RCSB PDB website provides better access to these data. These molecules are now search-able in the top-bar search, and we provide better reports and visualisation.
Access to Drug Targets in the PDB
For this release we integrated drug and drug target data from DrugBank (www.drugbank.ca). For example: look up Ibuprofen .
We also provide access to the Anatomical Therapeutic Chemical (ATC) Classification System, which is used for drug classification.
Better site navigation
We have re-designed our page header and given it a cleaner and simpler feel.
Uniprot Gene Names
We added a new search function for Gene names. Proteins that can be linked to PDB via Uniprot can now be identified by their associated gene annotations.
SCOP track in Protein Feature View
The Protein Feature View now has a new track - domain annotations from SCOP. Example: Obelin
This was just a quick summary of some of the new features. For a complete list, take a look at the What's new page.