Protein Data Bank Brookhaven

Preparation of a Brookhaven Protein Data Bank (PDB)-formatted [10] file containing the coordinates and appropriate names of all atoms, including all polar and aromatic hydrogens. 

To find appropriate empirical pair potentials from the known protein structures in the Brookhaven Protein Data Bank, it is necessary to calculate densities for the distance distribution of Ga-atoms at given bond distance d and given residue assignments ai,a2- Up to a constant factor that is immaterial for subsequent structure determination by global optimization, the potentials then ciiiergo as the negative logarithm of the densities. Since... 

We tested our new potential by applying a local optimization procedure to the potential of some proteins, starting with the native structure as given in the Brookhaven Protein Data Bank, and observing how far the coordinates moved through local optimization. For a good potential, one expects the optimizer to be close to the native structure. As in Ulrich et al. [34], we measure the distance between optimizer B and native structure A by the distance matrix error... 

D.R. Stampf, C.E. Felser and J.L. Sussman, PDBBrowse - a graphics interface to the Brookhaven Protein Data Bank, Nature 374 (1995), 572-574. 

L.L. Walsh, Navigating the Brookhaven Protein Data Bank, Gabos Communication 10 (1994), 551-557. 

HyperChem contains a database of amino and nucleic acid residues so you can quickly build polymers con laining these subunits. You can also read in structures in files from standard databases, such as the Brookhaven Protein Data Bank (see the HyperChem Reference Manual). 

PDB Databases Brookhaven Protein Data Bank Brookhaven National Laboratory... 

Fig. 3. Representation of the nine principal folds which recur in protein stmctures, where the codes of the representative proteins taken from the Brookhaven Protein Data Bank (PDB) (17) are given in parentheses (18) (1) globin (Ithb) (2) trefoil (lilb) (3) up—down (256b) (4) immunoglobulin folds...

The Brookhaven Protein Data Bank, PDB (http //www.pdb.bnl.gov), is the primary store of experimentally determined atomic coordinates of proteins. Each coordinate set has a unique identification code that can be... 

Molecule specifications can be entered by hand or be converted from the output of a graphics program. We ll perform a simple conversion here, converting the water molecule structure saved in Brookhaven Protein Data Bank (PDB) format. The file water. pdb in the quick subdirectory contains a PDB format structure for water. 

We ll look at a simple example of the latter method here, converting the water molecule structure saved in Brookhaven Protein Data Bank (PDB) format. 

All metric data for proteins are taken from the structures deposited in the Brookhaven Protein Data Bank. 

Fig. 7.23 Comparison of calculated and observed (x-ray ) mean N-C(a)-C bond angles for 37 proteins selected as described by Jiang et al. (1997,G). This reference is also the source of the values plotted, which are the region-average values, and . Regions of cb/ri-space and region numbering are explained in the lower graph. Experimental values (x-ray) were taken from the Brookhaven Protein Data Bank Chemistry Department, Building 555 Brookhaven National Laboratory, Box 5000, Upton N.Y. 11973-5000). The calculated values were obtained as described in the text.

Figure 6. Schematic representation of inositol monophosphate phosphatase (left) and inositol polyphosphate 1-phosphatase (right), showing the helical (green cylinders) and (3-sheet (yellow arrows) regions. The monophosphatase is complexed with lns(1)P (solid spheres) and Gd3+ (orange sphere) in the binding cleft and the polyphosphatase has two Mg2+ (lilac spheres) ions. (The coordinates were obtained from the Brookhaven Protein Data Bank).

Another major source are the amino acid sequences direcdy derived from protein sequencing. Thousands of such sequences have been detected by the SWISS-PROT curators in publications (or have been directly submitted by researchers to SWISS-PROT) and entered into the database. Protein sequences detected by the NCBI journal scan have also been included. For some proteins the Brookhaven Protein Data Bank (PDB) (Abola et al., 1996) is the only source for the sequence information. The PDB entries are checked regularly, and new SWISS-PROT entries were created whenever necessary. 

Molecular structure data bases are particularly useful in the analysis and engineering of zinc coordination polyhedra, and statistical results from the Brookhaven Protein Data Bank (Bernstein et al., 1977) and the Cambridge Structural Database (Allen et al., 1983) are presented... 

Currently, only a handful of examples of unique protein carboxylate-zinc interactions are available in the Brookhaven Protein Data Bank. Each of these entries, however, displays syn coordination stereochemistry, and two are bidentate (Christianson and Alexander, 1989) (Fig. 5). Other protein structures have been reported with iyw-oriented car-boxylate-zinc interactions, but full coordinate sets are not yet available [e.g., DNA polymerase (Ollis etal., 1985) and alkaline phosphatase (Kim and Wyckoff, 1989)]. A survey of all protein-metal ion interactions reveals that jyw-carboxylate—metal ion stereochemistry is preferred (Chakrabarti, 1990a). It is been suggested that potent zinc enzyme inhibition arises from syn-oriented interactions between inhibitor carboxylates and active-site zinc ions (Christianson and Lipscomb, 1988a see also Monzingo and Matthews, 1984), and the structures of such interactions may sample the reaction coordinate for enzymatic catalysis in certain systems (Christianson and Lipscomb, 1987). 

Fig. 5. (a and b) Two perpendicular orientations of direct carboxylate-zinc interactions retrieved from four metalloprotein structures contained in the Brookhaven Protein Data Bank. Orientation (a) represents the carboxylate group as found in Fig. 3. The coordination stereochemistry is syn for each example.

Fig. 9. Scatterplot of peptide carbonyl-metal ion interactions from the Brookhaven Protein Data Bank, with unidentate and bidentate examples indicated by circles and x s, respectively. [Reprinted with permission from Chakrabarti, P. (1990). Biochemistry 29 651-658. Copyright 1990 American Chemical Society.]...

Fig. 19. The carboxylate-histidine-zinc triad appears in the active site of carboxypeptidase A as Asp-142-His-69—and this interaction may contribute to zinc affinity in the metalloenzyme active site. Atomic coordinates were retrieved from the structure of the native enzyme (Rees et al, 1983) deposited in the Brookhaven Protein Data Bank.

Fig. 38. The zinc-thiolate cluster of the regulatory subunit of aspartate carbamoyl-transferase (Honzatko et al 1982). Coordinates are from the Brookhaven Protein Data Bank.

When including pair correlation 61,0% of the residues were correctly predicted in a 3 state model and 51,9% in a 4 state model. The database encompassed 74 proteins from the Brookhaven Protein Data Bank. 

After refining the protein structure the X-ray ciystallographer (or NMR spectroscopist) submits his refined stmcture to the Brookhaven Protein Data Bank. However, structures that have been solved as part of an industrial co-operation may be kept secret by an industry which has financed the study wholly or in part. Currently approximately 700 stractures are available, in the data bank but some of these have only been deposited as their sequence, whilst the data are being worked up. 

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