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Figure 6 | BMC Research Notes

Figure 6

From: Searching the protein structure database for ligand-binding site similarities using CPASS v.2

Figure 6

Illustrations of CPASS similarity scores using a representative aspartate aminotransferase protein (PDB ID 1art) and four different pyridoxal-5'-phosphate (PLP) dependent proteins: (a) aspartate aminotransferase (PDB ID 1asf) with a CPASS similarity of 82.73%, (b) LL-diaminopimelate aminotransferase (PDB ID 3ei8) with a CPASS similarity of 50.09%, (c) histidinol-phosphate aminotransferase (PDB ID 1gew) with a CPASS similarity of 42.13%, and (d) cysteine sulfinic acid decarboxylase (PDB ID 2jis) with a CPASS similarity of 30.85%, at the low end of the confidence limit for a functional relationship. The ligand defined binding sites are shown as licorice bonds where the molecular graphics images were produced using the UCSF Chimera (http://www.cgl.ucsf.edu/chimera) package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco [52]. The aspartate aminotransferase protein (PDB ID 1art) is colored blue in each panel, with PLP colored light blue. The other four PLP-dependent proteins in the binding site comparisons are colored red and the bound PLP is colored orange.

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