1YED

STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

Starting Models: 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGG1 FAB FRAGMENT (D.2.4)A [auth L],
B [auth A]
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IGG1 FAB FRAGMENT (D.2.4)C [auth H],
D [auth B]
226Mus musculusMutation(s): 0 
UniProt
Find proteins for P01868 (Mus musculus)
Explore P01868 
Go to UniProtKB:  P01868
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01868
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNB
Query on PNB

Download Ideal Coordinates CCD File 
E [auth L],
F [auth A]
4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
C13 H17 N2 O8 P
LNMNPGKCSJFAGN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.25α = 90
b = 104.79β = 90
c = 223.75γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

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: 2008-03-24
    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: 2024-11-06
    Changes: Data collection, Structure summary