1F3D | pdb_00001f3d

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), 0.224 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.203 (DCC) 

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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 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

Macromolecule Content 

  • Total Structure Weight: 95.5 kDa 
  • Atom Count: 7,035 
  • Modeled Residue Count: 868 
  • Deposited Residue Count: 872 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
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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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CATALYTIC ANTIBODY 4B2B [auth H],
D [auth K]		217Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.218 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.203 (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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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