1MFE

RECOGNITION OF A CELL-SURFACE OLIGO-SACCHARIDE OF PATHOGENIC SALMONELLA BY AN ANTIBODY FAB FRAGMENT

  • Classification: IMMUNOGLOBULIN
  • Mutation(s): 

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Recognition of a cell-surface oligosaccharide of pathogenic Salmonella by an antibody Fab fragment.

Cygler, M.Rose, D.R.Bundle, D.R.

(1991) Science 253: 442-445


  • PubMed Abstract: 
  • The 2.05 angstrom (A) resolution crystal structure of a dodecasaccharide-Fab complex revealed an unusual carbohydrate recognition site, defined by aromatic amino acids and a structured water molecule, rather than the carboxylic acid and amide side ch ...

    The 2.05 angstrom (A) resolution crystal structure of a dodecasaccharide-Fab complex revealed an unusual carbohydrate recognition site, defined by aromatic amino acids and a structured water molecule, rather than the carboxylic acid and amide side chains and a structured water molecule, rather than the carboxylic acid and amide side chains that are features of transport and other carbohydrate binding proteins. A trisaccharide epitope of a branched bacterial lipopolysaccharide fills this hydrophobic pocket (8 A deep by 7 A wide) in an entropy-assisted association (association constant = 2.05 x 10(5) liters per mole, enthalpy = -20.5 +/- 1.7 kilojoules per mole, and temperature times entropy = +10.0 +/- 2.9 kilojoules per mole). The requirement for the complementarity of van der Waals surfaces and the requirements of saccharide-saccharide and protein-saccharide hydrogen-bonding networks determine the antigen conformation adopted in the bound state.


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)
L
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)
H
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
L
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.300α = 90.00
b = 128.600β = 90.00
c = 79.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

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): 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