1F3D

CATALYTIC ANTIBODY 4B2 IN COMPLEX WITH ITS AMIDINIUM HAPTEN.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural evidence for a programmed general base in the active site of a catalytic antibody.

Golinelli-Pimpaneau, B.Goncalves, O.Dintinger, T.Blanchard, D.Knossow, M.Tellier, C.

(2000) Proc.Natl.Acad.Sci.USA 97: 9892-9895


  • PubMed Abstract: 
  • The crystal structure of the complex of a catalytic antibody with its cationic hapten at 1.9-A resolution demonstrates that the hapten amidinium group is stabilized through an ionic pair interaction with the carboxylate of a combining-site residue. T ...

    The crystal structure of the complex of a catalytic antibody with its cationic hapten at 1.9-A resolution demonstrates that the hapten amidinium group is stabilized through an ionic pair interaction with the carboxylate of a combining-site residue. The location of this carboxylate allows it to act as a general base in an allylic rearrangement. When compared with structures of other antibody complexes in which the positive moiety of the hapten is stabilized mostly by cation-pi interactions, this structure shows that the amidinium moiety is a useful candidate to elicit a carboxylate in an antibody combining site at a predetermined location with respect to the hapten. More generally, this structure highlights the advantage of a bidentate hapten for the programmed positioning of a chemically reactive residue in an antibody through charge complementarity to the hapten.


    Related Citations: 
    • Mechanism of an Antibody-Catalysed Allylic Isomerization.
      Goncalves, O.,Dintinger, T.,Lebreton, J.,Blanchard, D.,Tellier, C.
      (2000) BIOCHEM.J. 346: 691


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, B√Ętiment 34, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France. beatrice.golinelli@lebs.cnrs-gif.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATALYTIC ANTIBODY 4B2
L, J
219Mus musculusGene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus)
Go to UniProtKB:  A2NHM3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CATALYTIC ANTIBODY 4B2
H, K
217N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
K
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TPM
Query on TPM

Download SDF File 
Download CCD File 
J, L
2-(4-AMINOBENZYLAMINO)-3,4,5,6-TETRAHYDROPYRIDINIUM
C12 H18 N3
FWTCHDHYLQERRE-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.000α = 90.00
b = 87.200β = 97.60
c = 128.800γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-07-04
    Type: Version format compliance