Brookhaven Protein Databank

Data formats in the Brookhaven Protein Databank have become an intensively discussed topic in the last few years. The original PDB file format [17] was created in the late 1970s and maintained by the Research Collaboratory for Structural Bioinformatics [13]. In order to improve the organization of bibliographic... 

M. Hendlich, F. Rippmann, G. Barnick-el. BALI automatic assignment of bond and atom types for protein ligands in the brookhaven protein databank. /. Chem. Inf. Comput. Sci., 37, 774-778, 1997. 

Rg. 1.3 Parts of the disulphide-linked A and B chains of bovine insulin. (Reconstructed from data deposited in the Brookhaven protein databank, with permission of Professor D. L D. Caspar and the Biophysical Journal.)... 

Fig. 6.1 Ribbon model of bone morphogenetic protein-7. From the cystine knot emerge four antiparallel p-sheets, which form the finger 1 and 2 projections. An a-helix on the left-hand side of the knot lies perpendicular to the axis of the two fingers and forms the heel of the hand. (The cystine knot forming the core of the monomer consists of three disulphide bonds. Two disulphides form a ring through which the third disulphide passes.) (Reproduced with permission of the authors of ref. 2, and the Proc. Natl. Acad. Sci USA, from data filed with the Brookhaven protein databanks.)...

PSSD is a database that incorporates sequences of secondary-structure elements for all proteins with three-dimensional structures defined by experimental methods (such as NMR-Spectroscopy or X-Ray Crystallography) and for which structural data exist in the Brookhaven protein databank. 

Brookhaven Protein Databank refcodes ICDP, Ca-binding parvalbumin (Carp) 2CCY,... 

Brookhaven Protein Databank refcodes 6ACN, Aconitase (Pig) IPHH, p-Hydroxybenzoate hydroxylase (Pseudomonas fluorescens) 3FXN, Flavodoxin (Clostridium MP) 2TS1 Tyrosyl tRNA synthetase (Bacillus stearothermophilus), 2LIV, Leu-Ile-Val binding protein (E. coli). Short format references are given in Appendix B. 

Type V CSPs are protein phases. Because of the well established chemo- and stereospecificity of enzymes, a large number of experimentalists have adapted proteins in one form or another as stationary phases for chiral separations. The intermolecular forces responsible for analyte binding to these biopolymers are the same as for most other CSPs but the size and complexity of proteins makes them difficult to study computationally. One would think that with approximately 400 entries in the Brookhaven Protein Databank to select from, separation scientists would have used one of these proteins as a chiral selector and then use those atomic coordinates to carry out molecular modeling studies. Only one example has appeared in the literature where information from the PDB has been used to serve as a beginning point for molecular modeling of a protein CSP. In all other examples the CSP is viewed as having an unknown structure and Quantitative Structure-Enantioselective Retention Relationships (QSERRs) have been carried out. 

Brookhaven Protein Databank (PBD) Consists of relatively larger maeromoleeules related to the crystal coordinates of proteins. 

Enzyme-Reaction Database. We have built a database called the Enzyme-Reaction database for drug design based on amino acid sequence (Nishioka and Oda, unpublished). This database contains the following Items for each enzyme enzyme name Including common names, EC-number and reaction type classified by TUB, names of substrates, cofactors, inhibitors, and products, and entry codes in the NBRF sequence database and the Brookhaven Protein Databank. 

Figure 5.1 Stereo view of the active site of SNase. Coordinates are from the dataset 2SNS [ 15] of the Brookhaven Protein Databank. The positions of the two Ca ligated waters and the reacting water molecule have been indicated with small circles.

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