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From Protein Structure to Function with Bioinformatics.pdf

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11 <strong>Function</strong> Predictions of Structural Genomics Results 283Fig. 11.1 Enzyme active site template match illustrating the overlap between the bound S-inosylhomocysteine(SIB) ligand in Tm0936 (orange sticks; PDB entry 2plm) and the deoxycoformycin(DCF) ligand, an inosine analogue, bound <strong>to</strong> a template structure derived from an adenosinedeaminase (purple sticks; PDB entry 1a41). The bound zinc a<strong>to</strong>ms in both structures are displayedas overlapping spheres, the colouring following ligands bound <strong>to</strong> their respective proteins. Residuesfrom Tm0936 and adenosine deaminase are coloured blue and red, respectivelyFig. 11.2 Stereo view of the MSDfold superposition of the query structure (Tm0936, PDB entry2plm – coloured blue) <strong>with</strong> the structure used <strong>to</strong> generate the enzyme active site template (PDBentry 1a4l – coloured red). The additional secondary structure elements in the query protein canclearly be seen <strong>to</strong> the left of the image

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