Protein Data Bank entries from

Fig. 12. a/fi barrel domain of MR (based on Protein Data Bank entry 1 mnr). Important active site residues and the associated secondary structure elements are labeled and designated with arrows. From Babbitt and Gerlt (1997, Figure 1, p. 30592). 

Figure 3. Structure of IL-ip illustrating the location of receptor binding site A (residues 30, 32) and site B (residues 4, 6, 46, 56, 93,103,105). Site B residues R4 and L6 were mutated to alanine in mutant 1. The position of the K138C mutation is also indicated. Coordinates were taken from Protein Data Bank entry 2I1B (16). 

The putative structure of the BAR protease can be inferred from its sequence homology to chymosin (see Fig. 1.5 b Protein Data Bank entry ICMS). When the mutations that were found in the final engineered BAR variant are mapped onto this structure, approximately 50% of the mutations lie in or close to the substrate binding site of the protease, while the other 50% are found at distant sites in the protein. This distribution confirms that directed evolution processes efficiently generate mutations at relevant positions. 

From the coordinates of chain A, one of four azurin molecules in the unit cell of the Brookhaven Protein Data Bank entry "4AZU (21, 30). Molecular replacement and energy minimization were performed with Enzymix (36). 

The solution structure of OMTKY3 has been defermined using NMR by Hoogstra-ten et al. [55], and was obtained from the Protein Data Bank (entry lOMU). The first of the 50 conformers is used without further refinement of the overall structure. 

Fig. 13 Biomolecules used as enantioselective fluorescence sensors, (a) Blue fluorescent antibody 43 interacting with stilbene derivatives (structure from protein data bank, entry 1FL3 [124] (b) sensing of adenosine enantiomers by the DNA aptamer 44...

FIGURE 6.13 DNA is a double-stranded helical molecule composed of two intertwined sugar-phosphate backbone strands connected by the base pairs. Here, the elements are displayed by color carbon is green, nitrogen is blue, oxygen is red, and sulfur is orange. (Adapted from Protein Data Bank entry Ibna and rendered using Pymol.)... 

Image built upon coordinates from the 1EMB entry of the Protein Data Bank [84]... 

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. 

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). 

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. 

Figure 1. (a) View of the inside of the Methanol Dehydrogenase (MDH) enzyme with the active site in stick model. The solid surface represents the solvent-accessible MDH external surface showing the binding pocket, (b) View from the binding pocket of the entire MDH active site. Amino acids labels denote their location in the sequence obtained from the entry 1W6S (Methylobacterium Extorquens W3A1 ) of the Protein Data Bank. 

Fig. 1. Ribbon representation of an afiy unit of the crystallographic trimer of K. aerogeties urease. The Ni ions are located at the top of the a subunit (light gray) and are accessible from the solvent medium. The / and y subunits are depicted in dark and medium grey respectively. This drawing was prepared with Molscript [126] by A. Volbeda. Coordinates were obtained from entry 1KAU [16] from the Protein Data Bank [127]...

The design procedure described above was applied to the protein penicillopepsin, an aspartyl protease from Penicillium janthinellum. The coordinates for the protein were obtained from the Protein Data Bank (Jil) entry 2APP. The crystal structure was determined by James and Sielecki (11) at 1.8A resolution. 

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