NAR Molecular Biology Database Collection entry number 1866
Rathinavelan, Thenmalarchelvi; Reddy, Kunduru; Nair, Sanjana
Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana -502285, India.
Capsular polysaccharides or K antigens are one of the major virulent determinants in multidrug resistant Gram negative bacteria. These antigens play an important role in conferring pathogenicity to the microorganisms and are also essential in understanding the host pathogen interaction. We have developed an E. coli K antigen 3-dimensional structure database called EK3D, a manually curated database of 72 different E. coli K antigens. As the monosaccharide composition, linkage between the monosaccharides and their stereo isomeric forms differ between different K antigens, the database describes about group classification, capsular polysaccharide biosynthesis & their surface assembly mechanisms along with the structural information about K antigens. The K antigen structures are modeled based on the data derived from methylation studies and 1D (1H and 13C) & 2D NMR spectroscopy. The main purpose of this database is to enable an easy access to a given antigen structure from the listed ek-ids. We have also built K antigen multimer generation provision using rigid multimer modeling and flexible multimer modeling methods. In rigid multimer modeling, fixed inter and intra residue glycosidic torsion angles and a manually optimized helical twist angle are used for K antigen multimer generation. On the other hand, flexible multimer modeling utilizes virtual bond Cartesian coordinate transformation matrices method. In flexible multimer modeling, the user is given the flexibility to choose the desired inter-residue glycosidic torsion angles (phi and psi). These torsion angles are identical for the repeating units and may not represent the global minima of the molecule. Further, these models can serve as a good starting points for modeling studies. The user can generate the multimer by selecting the required K antigen and the preferred number of repeating units. The E. coli K antigen 3-dimensional structure database (EK3D) can be accessed through http://www.iith.ac.in/EK3D/.
Category: Genomics Databases (non-vertebrate)
Subcategory: Prokaryotic genome databases
Go to the abstract in the NAR 2016 Database Issue.
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