Materials and Methods (1zkd)

Determining the Structure

A protein search on PDB and NCBI Entrez was performed in identifying the structure of the given protein. Next, proteins with similar structures were identified using the DALI server. Dali server is a network service for comparing protein structures in 3D. The query protein structure is used to compare with those in the protein data bank. It will generate multiple alignment of structural neighbours. By comparing the 3D structures, it will hopefully reveal biologically interesting similarities that are not detectable by comparing sequences. 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 obtained using Pymol and Rasmol. Pfam and InterPro were also used to identify the domains of the protein.

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