The Protein Data Bank PDB

The PDB [7] covers biological macromolecules (proteins and nucleic acids) for which crystallographic results have been directly deposited with the compilers. The database currently contains 655 entries. Applications software is not distributed with the PDB. However, the data bank has been recast in a variety of forms for search and retrieval purposes [8,9]. Many molecular modelling systems (both commercial and academic in origin) can also read the PDB format. The database is compiled at the Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, USA. 

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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. 

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

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... 

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,... 

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.)... 

CAChe 5.0, available in 2002, includes a new, more powerful, semiempirical method that uses the PM5 Hamiltonian, a MOPAC 2002 offering, modeling of molecules with up to 20,000 atoms, the inclusion of all main group elements in one semiempirical method, and using MOPAC AMl-d, supports the transition metals Pt, Fe, Cu, Ag, Mo, V, and Pd. Researchers can now import and display, in 3D, proteins from the Protein Data Bank (PDB), optimize proteins, dock ligands, and model reactions on protein molecules. 

For updating the information presented in this chapter, a literature search on the keyword nitrogenase modified with structure, X ray, Mossbauer, iron sulfur cluster, or model compound will generate citations referring to the newest research results. A search of the Protein Data Bank (PDB) at the website address http //www.rcsb.org/pdb/ will yield the latest updates on X ray, NMR, and other submitted structural data. 

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