1MFA

STRUCTURE OF A SINGLE-CHAIN FV FRAGMENT COMPLEXED WITH A CARBOHYDRATE ANTIGEN AT 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution.

Zdanov, A.Li, Y.Bundle, D.R.Deng, S.J.MacKenzie, C.R.Narang, S.A.Young, N.M.Cygler, M.

(1994) Proc.Natl.Acad.Sci.USA 91: 6423-6427

  • DOI: 10.1073/pnas.91.14.6423

  • PubMed Abstract: 
  • We describe here the 1.7-A resolution structure of a single-chain antibody variable domain (scFv) molecule, based on the carbohydrate-binding antibody Se155-4, complexed with the trisaccharide ligand alpha-D-Gal(1-->2)[alpha-D-Abe(1-->3)]alpha-D-Manp ...

    We describe here the 1.7-A resolution structure of a single-chain antibody variable domain (scFv) molecule, based on the carbohydrate-binding antibody Se155-4, complexed with the trisaccharide ligand alpha-D-Gal(1-->2)[alpha-D-Abe(1-->3)]alpha-D-Manp1-->OMe, where Abe is abequose. The scFv expressed in Escherichia coli has the variable region light chain to heavy chain polarity with the domains connected by a 19-residue linker. Although the linker is partially disordered in the crystal, the packing of the molecules suggests a monomeric state of the scFv. The carbohydrate adopts a different conformation about the Man-Gal linkage than was observed previously in the Fab-trisaccharide complex. Instead of a direct hydrogen bond between O2Abe and O2Gal, these two atoms are bridged by a water molecule in the present complex.


    Related Citations: 
    • The Solution Structure of a Trisaccharide-Antibody Complex: Comparison of NMR Measurements with a Crystal Structure
      Bundle, D.R.,Baumann, H.,Brisson, J.-R.,Gagne, S.,Zdanov, A.,Cygler, M.
      () TO BE PUBLISHED --: --
    • Bacterial Expression and Secretion of Various Single-Chain Fv Genes Encoding Proteins Specific for a Salmonella Serotype B O-Antigen
      Anand, N.N.,Mandal, S.,Mackenzie, C.R.,Sadowska, J.,Sijurskjold, B.,Young, N.M.,Budle, D.R.,Narang, S.A.
      (1991) J.Biol.Chem. 266: 21874
    • Recognition of a Cell-Surface Oligo-Saccharide of Pathogenic Salmonella by an Antibody Fab Fragment
      Cygler, M.,Rose, D.R.,Bundle, D.R.
      (1991) Science 253: 442


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, Montreal, PQ.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)
L
127N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)
H
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMA
Query on MMA

Download SDF File 
Download CCD File 
H
O1-METHYL-MANNOSE
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
 Ligand Interaction
ABE
Query on ABE

Download SDF File 
Download CCD File 
H
ABEQUOSE
C6 H12 O4
KYPWIZMAJMNPMJ-KAZBKCHUSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
H
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.100α = 90.00
b = 61.000β = 90.00
c = 74.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-10-25 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Zdanov, A., Cygler, M.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance