1YEF

STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release.

Gigant, B.Charbonnier, J.B.Eshhar, Z.Green, B.S.Knossow, M.

(1997) Proc Natl Acad Sci U S A 94: 7857-7861

  • DOI: https://doi.org/10.1073/pnas.94.15.7857
  • Primary Citation of Related Structures:  
    1YEF, 1YEG, 1YEH

  • PubMed Abstract: 

    The x-ray structures of the unliganded esterase-like catalytic antibody D2.3 and its complexes with a substrate analogue and with one of the reaction products are analyzed. Together with the structure of the phosphonate transition state analogue hapten complex, these crystal structures provide a complete description of the reaction pathway. At alkaline pH, D2.3 acts by preferential stabilization of the negatively charged oxyanion intermediate of the reaction that results from hydroxide attack on the substrate. A tyrosine residue plays a crucial role in catalysis: it activates the ester substrate and, together with an asparagine, it stabilizes the oxyanion intermediate. A canal allows facile diffusion of water molecules to the reaction center that is deeply buried in the structure. Residues bordering this canal provide targets for mutagenesis to introduce a general base in the vicinity of the reaction center.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Unité Propre de Recherche 9063 Centre National de la Recherche Scientifique, Bat. 34, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENTA [auth L]219Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENTB [auth H]222Mus musculusMutation(s): 0 
Gene Names: Ighg
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: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.2α = 90
b = 78.2β = 90
c = 158.7γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
Agrovatadata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-03
    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