1YEC

STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural convergence in the active sites of a family of catalytic antibodies.

Charbonnier, J.B.Golinelli-Pimpaneau, B.Gigant, B.Tawfik, D.S.Chap, R.Schindler, D.G.Kim, S.H.Green, B.S.Eshhar, Z.Knossow, M.

(1997) Science 275: 1140-1142

  • DOI: https://doi.org/10.1126/science.275.5303.1140
  • Primary Citation of Related Structures:  
    1YEC, 1YED, 1YEE

  • PubMed Abstract: 

    The x-ray structures of three esterase-like catalytic antibodies identified by screening for catalytic activity the entire hybridoma repertoire, elicited in response to a phosphonate transition state analog (TSA) hapten, were analyzed. The high resolution structures account for catalysis by transition state stabilization, and in all three antibodies a tyrosine residue participates in the oxyanion hole. Despite significant conformational differences in their combining sites, the three antibodies, which are the most efficient among those elicited, achieve catalysis in essentially the same mode, suggesting that evolution for binding to a single TSA followed by screening for catalysis lead to antibodies with structural convergence.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et de Biochimie Structurales, CNRS, 91198 Gif sur Yvette Cedex, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENT (D2.3)A [auth L]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENT (D2.3)B [auth H]222Mus musculusMutation(s): 0 
UniProt
Find proteins for P01863 (Mus musculus)
Explore P01863 
Go to UniProtKB:  P01863
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01863
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.18α = 90
b = 78.18β = 90
c = 158.94γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary