1ZEA

Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structure of an anti-cholera toxin antibody Fab in complex with an epitope-derived D-peptide: a case of polyspecific recognition.

Scheerer, P.Kramer, A.Otte, L.Seifert, M.Wessner, H.Scholz, C.Krauss, N.Schneider-Mergener, J.Hohne, W.

(2007) J Mol Recognit 20: 263-274

  • DOI: https://doi.org/10.1002/jmr.838
  • Primary Citation of Related Structures:  
    1ZEA

  • PubMed Abstract: 

    The structure of a complex of the anti-cholera toxin antibody TE33 Fab (fragment antibody) with the D-peptide vpGsqhyds was solved to 1.78 A resolution. The D-peptide was derived from the linear L-peptide epitope VPGSQHIDS by a stepwise transformation. Despite the very similar amino acid sequence-the only difference is a tyrosine residue in position 7-there are marked differences in the individual positions with respect to their contribution to the peptide overall affinity as ascertained by a complete substitutional analysis. This is reflected by the X-ray structure of the TE33 Fab/D-peptide complex where there is an inverted orientation of the D-peptide as compared with the known structure of a corresponding complex containing the epitope L-peptide, with the side chains establishing different contacts within the binding site of TE33. The D- and L-peptide affinities are comparable and the surface areas buried by complex formation are almost the same. Thus the antibody TE33 provides a typical example for polyspecific binding behavior of IgG family antibodies.


  • Organizational Affiliation

    Charité-Universitätsmedizin Berlin, Institute of Biochemistry, Monbijoustr. 2, D-10117 Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
monoclonal anti-cholera toxin IGG1 KAPPA antibody, L chainA [auth L]216Mus musculusMutation(s): 0 
UniProt
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Entity Groups  
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UniProt GroupA2NHM3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
monoclonal anti-cholera toxin IGG1 KAPPA antibody, H chainB [auth H]216Mus musculusMutation(s): 0 
UniProt
Find proteins for Q921A6 (Mus musculus)
Explore Q921A6 
Go to UniProtKB:  Q921A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ921A6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
short synthetic D-amino acid peptide D2C [auth A]9synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.638α = 90
b = 108.862β = 90
c = 40.21γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-08-28
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-10-16
    Changes: Data collection
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description