Protein structural data

Protein structure data can be accessed through Protein Data Bank at URL httpy/www.rcsb.org/pdb some structural data, designated as SM can be assessed... 

Protein Explorer is a knowledge base with introductory information on many topics about protein structure, such as the origins and limitations of 3D protein structure data, specific oligomers vs. crystal contacts, hydrogen bonds, cahon-pl interactions, etc. Protein Explorer is more user-friendly than the comparable software RASMOL, also available on servers such as ExPASy. 

The text has been substantially revised, many new examples incorporated and errors corrected. A substantial new chapter dealing with supramolecular chemistry has been incorporated. Once again, a deliberate decision was made to try to limit references to the secondary rather than the primary literature. Where structural data have been presented, the use of the files of the Cambridge Crystallographic Data Centre and the Brookhaven Protein Structure Data Base are gratefully acknowledged. 

Tainer, J. A. et al. in 250D Cu.Zn-Superoxide Dismutase Complete Atomic Coordinates (eds.) Richardson, D. C. and Richardson, J. S., Brookhaven Protein Structure Data Bank 1980... 

Hubbard, T. J., et al., SCOP, Structural Classification of Proteins database applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr D Biol Crystallogr, 1998. 54(1 (Pt 6)) p. 1147-54. 

S. J. Wodak and M. J, Rooman, Nature (London), 335,45(1988). Identification of Predictive Sequence Motifs Limited by Protein Structure Data Base Size. 

Wild into Mutated W> M). Frequently the interactions with the environment induce considerable pKa shifts resulting in change of the aminoacid protonation state. Unfortunately, most of available protein structural data does not contain any information regarding proton positions, except for few neutron diffraction and NMR structures only. 

However, even if the theoretical data were perfect, the comparison with and interpretation of the experimental findings would still be difficult due to the large uncertainties of the data. Protein structural data have relatively large error bars for bond distances. It is clear from the discussion above that the use of theoretical structure data leads to a more consistent interpretation of the spectroscopic data. This is maybe not so surprising, since we expect the theoretical structures to be more accurate. Also the interpretation of the spectroscopic data is ambiguous, as they are based on a Gaussian fit, which has to assume the number of bands in the spectrum. We saw that for plastocyanin a weak band (at 18 700 cm" ) has no counterpart in the theoretical spectrum and is most probably an artifact. 

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