E. coli K antigen 3-dimensional structure database
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E. coli K antigen 3-dimensional structure database
metasource: Fairsharing.org
version: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
EK3D
metasource: Fairsharing.org
version: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
E. coli K antigen 3-dimensional structure database
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
EK3D
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
E. coli K antigen 3-dimensional structure database
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
EK3D
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
EK3D - an E. coli K antigen 3-dimensional structure database is a repository of 72 E. coli K antigens that provides information about the sugar composition, epimeric & enantiomeric forms and linkages between the sugar monomers.
Description
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EK3D - an E. coli K antigen 3-dimensional structure database is a repository of 72 E. coli K antigens that provides information about the sugar composition, epimeric & enantiomeric forms and linkages between the sugar monomers.
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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/.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://www.iith.ac.in/EK3D/Webpage
More detailed information about this field from each metasource.
http://www.iith.ac.in/EK3D/
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
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EK3D: an E. coli K antigen 3-dimensional structure database
PMID: 26615200
metasource: Fairsharing.org
version: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkv1313
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
EK3D: an E. coli K antigen 3-dimensional structure database
PMID: 26615200
metasource: Fairsharing.org
version: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkv1313
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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EK3D: an E. coli K antigen 3-dimensional structure database
PubMed citations: 6.
6 articles citing: EK3D: an E. coli K antigen 3-dimensional structure database
Opportunities and Challenges of Bacterial Glycosylation for the Development of Novel Antibacterial Strategies. PMID:34630370
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains. PMID:33028855
Targeting the Sugary Armor of Klebsiella Species. PMID:31781512
E. coli Group 1 Capsular Polysaccharide Exportation Nanomachinary as a Plausible Antivirulence Target in the Perspective of Emerging Antimicrobial Resistance. PMID:28217109
Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin. PMID:27320406 - http://dx.doi.org/10.1093/nar/gkv1313
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Tags
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antigen
metasource: Fairsharing.org
version: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
antigen
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: EK3D ; E. coli K antigen 3-dimensional structure database; DOI: https://doi.org/10.25504/FAIRsharing.syayhh; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
antigen structure genomics prokaryotic genome
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