Generation of 3D structures of E. coli K antigens

Nomenclature used in chemical representation of monosaccharides in EK3D

  OAc : O acetylation

  NAC : N acetylation

  Pyr : Pyruvate

  Glcp : Glucopyranose

  Galp : Galactopyranose

  Manp: Mannopyranose

  Quip: Quinovopyranose

  Fucp: Fucopyranose

  Rhap: Rhamnopyranose

  Galf: Galactofuranose

  Ribf: Ribofuranose

  Fruf: Fructofuranose

  GlcNAc : N Acetyl Glucosamine

  GalNAc : N Acetyl Galactosamine

  ManNAc : N Acetyl Mannosamine

  FucNAc : N Acetyl Fucosamine

  KDOp :KDO pyranose form (KDO : 3-Deoxy-D-manno-oct-2-ulosonic acid )

  KDOf :KDO furanose form

  SugarP: 2,3-diacetamido-2,3,6-trideoxy-beta L-Mannopyranose

  SugarS: 6-O-Acetyl-4-deoxy-hexulosonic acid

  Gro : Glycerol

  Ser : Serine

  Thr : Threonine

Schematic representation of monosaccharides in EK3D

  1. Anomeric form (alpha/beta) is indicated at the top right of the sugar

  2. Isomeric form (L/D) is indicated at the bottom left of the sugar

  3. Furanose sugars are indicated by "f" inside the sugar (ex. Ribose in the table below)

The schematic representation has been adopted from the glycan representation developed by the Consortium for functional glycomics (CFG)


- Berger, O., McBride, R., Razi, N. & Paulson, J. (2008) "Symbol Notation Extension for Pathogen Polysaccharides", The Scripps Research Institute, Consortium for Functional Glycomics.

- Varki, A., Cummings, R.D., Esko, J.D., Freeze, H.H., Stanley, P., Marth, J.D., Bertozzi, C.R., Hart, G.W. and Etzler, M.E. (2009) Symbol nomenclature for glycan representation. Proteomics, 9, 5398-5399.

Four letter monosaccharide code used in EK3D

Convert to EK3D format :

Multimer generation

Rigid multimer modeling in EK3D

- In rigid multimer modeling (RMM), both the inter- and intra-repeat glycosidic torsion angles are fixed

- The user can select the required K antigen and input the preferred number of repeating units

- In the above example, a trimer of K32 is generated

Flexible multimer modeling in EK3D

- In flexible multimer modeling (FMM), the intra-repeat torsion angle is fixed

- The user can choose the inter-repeat torsion angles of their choice along with the number of repeating units

- In the above example generation of a trimer of ek32 with two different sets of torsion angles is shown

- The figure on the top right depicts the virtual bond coordinate transformation method followed in FMM considering two repeating units of K32 (where the   (i-1)th and ith residues are represented in blue and green respectively)

- Dotted red line indicates the virtual bond connecting inter-repeating unit glycosidic oxygens

- The Cartesian coordinate system of each individual repeating unit is affixed in such a way that the X axis lies along the virtual bond

- The Y axis is chosen to be in a plane defined by the virtual bond and the preceding chemical bond [O(1)i-C(4)i] so as to make an acute angle with the   preceding bond

- Direction of the Z axis is chosen to complete the right handed coordinate system

- θ is the supplement of the bond angle C(1)i-1-O(1)i-C(4)i

- η and ζ are the angles formed by C(4)i-O(1)i-O(1)i+1 and C(1)i-1-O(1)i-O(1)i-1 respectively

- φ and ψ are the glycosidic dihedral angles representing the rotation around atoms O(5)i-1-C(1)i-1-O(1)i-C(4)i and C(1)i-1-O(1)i-C(4)i-C(3)i respectively

Definition of φ and ψ

- φ and ψ are defined in the direction of decremental order of the main chain residue number

- For a j-k linkage :

φ is the dihedral angle formed by O(5)i-1-C(j)i-1-O(j)i-C(k)i

ψ is the dihedral angle formed by C(j)i-1-O(j)i-C(k)i-C(k-1)i

- NOTE : j, k represent the atom numbers, while i, i-1 represent the repeating units

© Indian Institute of Technology Hyderabad, India
TR Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, India