Methods for Structure Analysis

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The research structure of PDB file (1RU8) was obtained from RSCB Protein Data Bank. For visualization, the PDB file retrieved was then uploaded into PyMOL software to visualize the 3-D structure and for other analysis. Moreover, in order to obtained proteins with similar structure, DALI server was used for our protein of interest 1RU8 where the outcome of the results give indication of other structural neighbours that have degree of similarity in structures. Two protein, 2NZ2 and 3BL5, that has the highest similarity (z-score) was chosen for comparison and analysis in terms of structural alignment and cleft size and volume similarities with 1RU8. Structural similarities are important in determining significant structures that may not be detected by sequence alignment. Profunc, PDBsum, InterPro, and CASTp was used in identifying the details on the secondary structure, ligands and cleft of the proteins.