The Protein Data Bank

The ftCSB FOB provides o variety of tools and resources for studying the structures of biologicot macromotecutes and their reiattonships to seouence, function and disease. 

The ACSB Is a member of the wwPDB whose mission is CO ensure that (he pdb archive remains an iniemacionai resource with uniform data. 

Information about compatible browsers cart be found here. 

FIGURE 19.11 The Protein Data Bank home page. 

FIGURE 19.12 An image of citrate synthase, downloaded from the Protein Data Bank. 

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As a template for an intermediate conformation of protein kinase, the crystal structure of the binary complex of cAPK with adenosine (Ibkx.pdb in the Protein Data Bank) was used. As templates for open conformations... 

F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E. Meyer, M.D. Bryce, J.R. Rogers, O. Kennard, T. Shikanouchi and M. Tasumi, The protein data bank A computer-based archival file for macromolecular structures, J. Mol. Biol. 112 (1977), 535-542. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

Having looked at the general structure of PDB files, let us now examine a sample PDB file. The file represents the structure of r conotoxin PNll polypeptide (PDB ID Ipcn) and was retrieved from the Protein Data Bank [53]. Figure 2-109 shows the 3D structure of the molecule. 

The fir.-fit line of the file (see Figure 2-110) - the HEADER record - hold.s the moleculc. s classification string (columns 11-50), the deposition date (the date when the data were received by the PDB) in columns 51-59, and the PDB (Dcode for the molecule, which is unique within the Protein Data Bank, in columns 63-66. The second line - the TITLE record - contains the title of the experiment or the analysis that is represented in the entry. The subsequent records contain a more detailed description of the macromolecular content of the entiy (COMPND), the biological and/or chemical source ofeach biological molecule in the entiy (SOURCE), a set ofkeywords relevant to the entiy (KEYWDS). information about the experiment (EXPDTA), a list of people responsible for the contents of this entiy (.AUTHOR), a history of modifications made to this entiy since its release (REVDAT), and finally the primaiy literature citation that describes the experiment which resulted in the deposited dataset ()RNL). 

As this short example shows. PDB files use different syntax for different records and both writing and reading such files require much effort. Another problem is the extensibility of this format to handle new kinds of information, which further complicates the file structure. The Protein Data Bank has been faced with the consequences - the existing legacy data comply with several different PDB formats, so they are not uniform and they arc more difEcuh to handle (145, 155, 157]. As mentioned in Section 2,9.7.1, there is a much more flexible and general way of representing molecular structure codes and associated information - the STAR file format and the file formats based on it. 

D structures of macromolecules, especially proteins and nudeic adds, are found in the Protein Data Bank (PDB) [27]. 

Bernstein F C, T F Koetzle, G J B Williams, E Meyer, M D Bryce, J R Rogers, O Kennard, T Shikanouchi and M Tasumi 1977. The Protein Data Bank A Computer-Based Archival File for Macromolecular Structures. Journal of Molecular Biology 112 535-542. 

The Protein Data Bank PDB ID 1A71 Colby T D Bahnson B J Chin J K Klinman J P Goldstein B M Active Site Modifications m a Double Mutant of Liver Alcohol Dehydrogenase Structural Studies of Two Enzyme Ligand Com plexes To be published... 

Page 1093 (Figure 26 9c) is adapted from crystallographic coordinates deposited with the Protein Data Bank PDB ID ICLE Ghosh D Wawrzak Z Pletnev V Z Li N Kaiser R Pangbom W Jornvall H Erman M Duax W L Structure of Un complexed and Linoleate Bound Candida Cholesterol Esterase To be published... 

Page 1171 (Figure 28 7) is adapted from crystallograpliic coordinates deposited with The Protein Data Bank PDB ID lAOl Luger A Mader W Richmond R K Sargent D F Richmond T J Crystal Structure of the Nucleosome Core Particle at 2 8 A Resolution Nature 1997 V 389 251... 

Software for structure determination and analysis at the Protein Data Bank http //www.rcsb.org/pdb/Modeling... 

The first requirement for threading is to have a database of all the known different protein folds. Eisenberg has used his own library of about 800 folds, which represents a minimally redundant set of the more than 6000 structures deposited at the Protein Data Bank. Other groups use databases available on the World Wide Web, where the folds are hierarchically ordered according to structural and functional similarities, such as SCOP, designed by Alexey Murzin and Cyrus Chothia in Cambridge, UK. 

Bernstein, F.C., et al. The protein data bank a computer-based archival file for macromolecular structures. 

Page 1048 (Eigure 25.8) is adapted from crystallographic coordinates deposited witli the Protein Data Bank. PDB ID 4TE4. Sakon, J., Irwin, D., Wilson, D. B.,... 

Pages 1049 (Eigure 25.9) and 1050 (Eigure 25.10) are adapted from crystallographic coordinates deposited with The Protein Data Bank, PDB ID 1C58. Gessler, K, Uson, L, Takahan, T., Krauss, N., Smith,... 

Most packages will happily take Cartesian coordinates or Z-matrices, but you ought to be aware of the Z-matrix. The point is that Cartesian coordinates can be obtained from sources such as the Protein Data Bank (these come in files with. pdb or. ent extensions). 

The structure of human muscle fructose-1,6-bisphosphate aldolase, as determined by X-ray crystallography and downloaded from the Protein Data Bank. (PDB ID 1ALD Gamblin, S. J., Davies, G. J., Grimes, J. M., Jackson, R. M., Littlechild, J. A., Watson, H. C. Activity and specificity of human aldolases. J. Mol. Biol. v219, pp. 573-576, 1991.)... 

How Do Enzymes Work Citrate Synthase 1043 Focus On... The Protein Data Bank 1048... 

Berman HM, Westbrook J, Feng Z et al (2000) The Protein Data Bank. Nucleic Acids Res 28 235-242... 

The Pe-Pe distances in the published article, 2.64, 2.71, 2.73 A, differ significantly from those deduced from the structure deposited in the Protein Data Bank. 

Table III reports structural statistics relative to the solution structures of iron-sulfur proteins available from the Protein Data Bank (118). The lowest percentage of residue assignment occurs for oxidized Synechococcus elongatus Fd (119). The highest percentage of proton assignment is instead obtained for oxidized E. halophila HiPIP, with a value as high as 95% (120). A close figure was also obtained for the reduced protein (94%). In the latter case, such high values are obtained also thanks to the availability of labeled...

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