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 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.190 (DCC) 

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Ligand Structure Quality Assessment 

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This is version 1.4 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: https://doi.org/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. 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.


  • 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATALYTIC ANTIBODY 4B2A [auth L],
C [auth J]
219Mus musculusMutation(s): 0 
UniProt
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2NHM3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CATALYTIC ANTIBODY 4B2B [auth H],
D [auth K]
217Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.218 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.190 (DCC) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TPMClick on this verticalbar to view details

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
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary