Materials and Methods - 2qgnA

Determination of Structure

A protein search on PDB and NCBI Entrez was performed in order to obtain the sequence of the given protein. Data of given protein was retrieved and then uploaded into PyMOL software to construct the 3-D structure as well as enable further analysis. Next, proteins with similar structures were identified using the DALI server. Results from the server generated an an outcome of other structural neighbours which confer a considerable degree of similarity in structure. By comparing the 3D structures, biologically interesting similarities that may not have detectable by sequence alignment are exposed. A CE comparison was performed among the identified structures as it uses databases and tools for 3D Protein structure comparison and alignment. It calculates structural alignment for two chains. Surface properties of the given proteins were analysed using Pymol. Profunc, PDBsum and InterPro were also utilised to identify the domains, ligands and clefts on the protein.