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 

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Ligand Structure Quality Assessment 


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 U S A 97: 9892-9895

  • DOI: 10.1073/pnas.97.18.9892
  • Primary Citation of Related Structures:  
    1F3D

  • 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. The location of this carboxylate allows it to act as a general base in an allylic rearrangement ...

    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, Bâtiment 34, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France. beatrice.golinelli@lebs.cnrs-gif.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATALYTIC ANTIBODY 4B2C [auth J], A [auth L]219Mus musculusMutation(s): 0 
Gene Names: IgkcIgk-C
UniProt
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CATALYTIC ANTIBODY 4B2B [auth H], D [auth K]217Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPM (Subject of Investigation/LOI)
Query on TPM

Download Ideal Coordinates CCD File 
E [auth L], F [auth J]2-(4-AMINOBENZYLAMINO)-3,4,5,6-TETRAHYDROPYRIDINIUM
C12 H18 N3
FWTCHDHYLQERRE-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth K]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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 = 45α = 90
b = 87.2β = 97.6
c = 128.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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