How a protein interacts with other biological molecules depends on its molecular structure, which can include such features as active sites, folds, loops, knobs, pits, ridges, and valleys. They also have produced a general method for rapidly finding the similarities in protein structures. The PDB archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, crystallographic structure factors, and nuclear magnetic resonance experimental data. Users also can define their own input sets of compounds or entities to form a custom list for interrogation. These different views reveal information about external and internal structure, much as a snapshot and a doctor's X-ray convey different information.
All images show the same viewing orientation.
Secondary sheet structures are rendered in orange. The current database is based on the same binary index files as used in SDSC's WPDB, a compact variant of the PDB distributed on CD-ROM that can be accessed on Windows PCs. Within any protein database, understanding the relationships between structures and functions depends on finding substructures active sites, specific folds and fragments, or regions with distinctive geometrical or physical properties. While substructure recognition has been actively researched, until recently biologists had no easily accessible, automated resource. A researcher might want to know, for example, what motifs or folds one protein has in common with other 3-D protein structures, even if there is low sequence similarity.