Protein Data Bank downloading structures from

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.)... 

Another way to get a structure into the computer is to import (read) a molecule file containing the atomic co-ordinates (and perhaps other atomic and molecular information) into your program. Unfortunately, there is no single standard file format that all programs use. However, some of the commonly encountered formats include those of SYBYL MOL2 files and Protein Data Bank (PDB) files. There are also free programs available for download from the World Wide Web that can interconvert the numerous file formats still in use. 

The Protein Data Bank (PDB, http //www.rcsb.org/pdb/) is the de facto repository for macromolecular structures resolved by NMR or diffraction methods [42]. The structures of many protein-ligand complexes have been resolved and their atomic coordinates can be downloaded from the PDB web portal for further analysis. 

The common atomic coordinate files for 3D structure in biochemistry is PDB format. The pdb files of polysaccharides, proteins, and nucleic acids can be retrieved from the Protein Data Bank at RCSB (http //www.rcsb.org/pdb/). On the home page (Figure 4.15), enter PDB ID (check the box query by PDB id only ) or keywords (check the box match exact word ) and click Find a structure button. Alternatively, initiate search/retrieval by selecting SearchLite. On the query page, enter the keyword (e.g., the name of ligand or biomacromolecule) and click Search button. Select the desired entry from the list of hits to access Summary information of the selected molecule. From the Summary information, select Download/Display file and then PDB Text and PDB noncompression format to retrieve the pdb file. In order to display 3D structure online, choose View structure followed by selecting one of 3D display options. The display can be saved in. jpg or. gif image format. 

Computational results were obtained using Spartan 08 (Wavefunction Inc., Irvine, CA) and software programs from Accelrys Software Inc. with graphical displays generated by the Discovery Studio Visualizer. Where protein structures have been downloaded from the RCSB Protein Data Bank the full references and PDB IDs have been given. I wish to acknowledge the use of the Chemical Database Service at Daresbury for access to other crystal structures. Again, full primary sources can be found in the references. 

Crystal structures are stored in formatted text files called "PDB" files. These files can be freely downloaded from the RCSB Protein Data Bank at http //www.pdb.org. Information on how to search and navigate the PDB is available on the PDB home page. 

Figure 4.5. Crystal structure of the self-compleuientary DNA oligonucleotide 5 -CATGGCCATG-3, downloaded from the Protein Data Bank (ID 126D) and visualized in RasMol [58]. (See color plates).

Figure 4.15, Crystal structure of the nucleosome, downloaded from the Protein Data Bank (ID lAOI) and visualized in ribbon format in Rasmol [117]. (Top) Front view. (Bottom) Side view. The eight histone proteins are in greens and blues, and DNA double helix, wrapped around the histone core 1.5 times, is in orange-red and gold. (See color plates).

Figure 5.5 Retrieval of protein structure from Protein Data Bank The atomic coordinates of protein three-dimension structures can be retrieved from PDB (http //www.rcsb.org/pdb) by entering PDB id (e.g. IRNO) or keyword (e.g. pancreatic ribonuclease). The query search returns a list of hits from which the desired PDB file can be selected (click Explore), then viewed (select View structure as shown), analyzed (select Structure neighbor. Geometry or Sequence detail) and retrieved (select Download/Display file).

PROCHECKcan be downloaded from the following web site http //www.biochenL ucl.ac.uk/ roman/procheckyprocheck.html. To run PROCHECK, one simply types procheck mycoordinates.pdb resolution limit , where mycoordinates.pdb should contain coordinates of your refined protein structure in standard Protein Data Bank (PDB) format, and resolutionjimit should correspond to the high resolution limit of the data (in A) used in the refinement. Alternatively, one can submit coordinates to either of two websites the SAVS server or the PDB validation server (www.deposit.pdb.org/validate/). For additional information, consult the PROCHECK manual www.biochem.ucl.ac.uk/ roman/procheck/manual/. 

FIGURE 9.61 Molecular structures of a 1,4-p-endoglucanase (a) and 1,4-p-exoglucanase (b) showing the cleft and tunnel features, respectively. These drawings were prepared from files downloaded from the Brookhaven Protein Data Bank (http //pdb.pdb.bnl.gov). (a) (ICEC) and (b) (3CBH, Ca skeleton) were rotated to reveal the cleft and tunnel, respectively, with RasMol, Version 2.5, by Roger Sayle, freeware available from the Brookhaven National Laboratory web site. 

The structure of human muscle fructose-i,6-bisphosphate aldolase, as determined by X-ray crystallography and downloaded from the Protein Data Bank. 

In the Chapter 19 Lagniappe, we discussed how to access enzyme structural data from the Protein Data Bank. Once the data for a specific enzyme have been located, it s then possible to visualize, manipulate, and study the structure. You can do this either by downloading the data file to your own computer and opening it with a free visualization program, such as DeepView (Swiss PDB Viewer)... 

The structure of E.coli heat-labile enterotoxin determined by X-ray crystallography and downloaded from the Protein Data Bank (see page 700). The protein has seven subunits—that is seven protein chains (Section 22.16). Five of them (blue, green purple, etc.) attach to a cell membrane. The toxin uses the red helical spike to deliver the catalytic subunit (orange) into the cell. The red and gray space-filling model is a protein side chain that acts as a base catalyst (Section 23.9). This toxin is responsible for what is known as traveler s diarrhea. 

---