RCSB Protein Data Base

Tertiary Structure of Proteins The tertiary structure of a protein refers to how the alpha helices and beta sheet portions of a polypeptide chain are folded into a compact or globular structure. Two-dimensional representations of the three-dimensional tertiary structures of proteins are, well, pretty two dimensional. If you want to better understand tertiary structure, you can view interactive, three-dimensional models of a large variety of proteins at the RCSB Protein Data Base at http //www.rcsb.org. 

Fig. 1. Resolution histogram in resolution bins of 0.25 A for the hyperthetmophilic proteins (solid bars) listed in Table I and for the entire Protein Data Base (PDB) [cross-hatched bars J. Sussman, D. Lin, J. Jiang, N. Manning, J. Prilusky, O. Ritter, and E. Abola, Acta Crystallogr. D54,1078 (1998) Research Collaboratory for Structural Bioinformatics PDB, http //www.rcsb.oig/pdb/], as estimated in October, 1999 from http //db2.sdsc.edu/moose/images/summary.gif.

FIGURE 4-22 Organization of proteins based on motifs. Shown here are just a small number of the hundreds of known stable motifs. They are divided into four classes all a, all /3, all3, and a + /3. Structural classification data from the SCOP (Structural Classification of Proteins) database (http //scop.mrc-lmb.cam.ac.uk/scop) are also provided. The PDB identifier is the unique number given to each structure archived in the Protein Data Bank (www.rcsb.org/pdb). The a//3 barrel, shown in Figure 4-21, is another particularly common a/fS motif. 

Experimental protein folding data based on both x-ray crystallographic and NMR results are available online through the Protein Data Bank (PDB, http //www.rcsb.org/pdb). 

Kennard, T. Shimanouchi, and M. Tasumi,/. Mol. Biol., 112,535 (1977). The Protein Data Bank A Computer-Based Archival File for Macromolecular Structures. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, Nucleic Acids Res., 28, 235 (2000). The Protein Data Bank, www.rcsb.org/pdb/. 

O. Kennard, T. Shimanouchi, and M. Tasumi,/. Mol. Biol., 112, 535 (1977). The Protein Data Bank A Computer-Based Archival File for Macromolecular Structures, http // www.rcsb.org/pdb. 

With the rapid advances in macromolecule crystallography, the PDB (http //www.rcsb.org/pdb/) currently contains about 12,600 macromolecular NMR or crystal structures. While this may not represent all macromolecular structures, it does represent the large majority. Most of the major scientific journals require simultaneous deposition of macromolecular crystal data into the PDB as the journal article is published. Besides structural proteins, and the classic crystal structures such as hemoglobin and lysozyme, the data base includes many enzymes or representative enzymes from classes that could be good targets for chemotherapy. 

PDB The Protein Data Bank, originally compiled at Brookhaven National Laboratory and currently distributed from http //www.rcsb.org, contains X-ray diffraction and NMR-based structural data of macromolecular structures such as proteins, nucleic acids, and entire viruses. The PDB is the primary structural databank for the 3-D coordinates of macromolecules and freely accessible on-line. 

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