RCSB protein data bank

RCSB Protein Data Bank, from the Research Collaboratory for Structural Bioinformatics,... 

RCSB Protein Data Bank 1EX7, enzyme with a non-acetylated N terminus in a complex with GMP [22]) [7-10, 13, 19, 18, 22]... 

S100A13 differs from the other family members in its very broad expression pattern and the absence of a surface-exposed hydrophobic patch in the Ca2+-saturated state. Its 3-dimensional structures (Sivaraja et al., 2005) deposited in the RCSB Protein Data Bank supports the unique properties of this S100A13 protein. 

FIGURE 3.4.3 Cartoon representation of the three-dimensional structures of (a) Pru av 1 determined by NMR and (b) Api g 1 determined by x-ray crystallography. Pru av 1 represents an overlay of 22 chains retrieved from RCSB Protein Data Bank (accession number le09), Api g 1 (2bk0). Highly flexible loops between (33-(34 and (37-a3 structures are depicted in blue, (3-sheets in green, and a-helices in red. 

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. 

At this writing, the three-dimensional sttuctures of eight different naturally occurring type 1 copper proteins are known. These include the cupredoxins plastocyanin at 1.33 A resolution (pdb code 1 PTC), azurin at 1.8 A (pdb code 2AZA), pseudoazurin at 1.55 A (pdb code IPAZ), amicyanin at 1.3 A (pdb code lAAC), auracyanin at 1.55 A (pdb code IQHQ), rusticyanin at 1.9 A (pdb code IRCY), and the phytocyanins cucumber basic protein at 1.8 A (pdb code2CBP), and stellacyanin at 1.6 A (pdb code IJER) Atomic coordinates for these and all other single-domain type 1 copper proteins are available from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) and can be accessed online at www.rcsb.org/pdb/. 

At about the same time, Terp et al. [11] used GRID/CPCA to analyze 10 MMPs with the intention of highlighting regions that could be potential sites for obtaining selectivity. Some of the structures were retrieved from the RCSB protein data bank [53], others were obtained through homology modeling [56]. To facilitate the analysis, the authors used the cut-out tool to focus on each of the six subsites in turn. 

RCSB Protein Data Bank. Nature of 3D Structural Data, http //www.rcsb.org/pdb/static.do p=general information/about pdb/nature of 3d structural data.html. 

The RCSB protein data bank redesigned web site and web services. Nucleic Acids Res 39 D392-D401... 

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. 

RCSB Protein Data Bank (PDB). Research Col laboratory for Structural Bioinformatics (RCSB). URL http //www.rcsb.org/ pdb/. Repository for the processing and distribution of experimentally determined three-dimensional macromolecular structure data. 

Structural model of the complex of the 3,6,9-trisubstituted acridine ligand (3) with the intramolecular basket quadruplex structure of the human telomeric sequence, (a) End-stacking with the terminal G-tetradpermits the substituent at the 9-position to interact with the flexible TTA loop structure in a specific manner, (b) X-ray structure of the complex of a di-substituted aninoalkylamido acridine (4) with the dimeric hairpin quadruplex structure derived from the Oxytricha nova sequence d(GGGGTTTTGGGG)2. The drug end-stacks and interacts extensively with the thymine loop ((a) Adapted from ref 25 and (b) from RCSB Protein Data Bank co-ordinates ILIH (ref 49)). 

The RCSB Protein Data Bank Microsoft Internet Explorer... 

RCSB Protein Data Bank http //www.rcsb.org/pdb... 

Maltseva, N., Kim, Y., Kwon, K., Joachimiak, A., and Anderson, W.F. RCSB Protein Data Bank (PDB entries 3HYL and 3M49, submitted 06/2009 and 04/2010). 

The RCSB Protein Data Bank (www.pdb.org) is the repository of more than 57,000 three-dimensional structures that have been determined by X-ray crystallography (shown on the opening page of this chapter) or multidimensional NMR (Section 15.22). The structures are publicly available for download in a PDB format. The structures can be visualized and manipulated with free programs such as Visual Molecular Dynamics (http //www.ks.uiuc.edu/Research/ vmd/) or Chimera (http //www.cgl.ucsf.edu/chimera). 

PDB. (2010). RCSB protein data bank. http //www. rcsb.org/pdb. Accessed 02 July 2011. 

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