EK3D: an E. coli K antigen 3-dimensional structure database

Nucleic Acids Res. 2016 Jan 4;44(D1):D675-81. doi: 10.1093/nar/gkv1313. Epub 2015 Nov 28.


A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host-pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, Bacterial / chemistry*
  • Databases, Chemical*
  • Escherichia coli / immunology*
  • Escherichia coli / pathogenicity
  • Internet
  • Models, Molecular
  • Polysaccharides, Bacterial / chemistry*
  • Protein Conformation
  • Virulence Factors / chemistry


  • Antigens, Bacterial
  • Polysaccharides, Bacterial
  • Virulence Factors