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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/science.275.5303.1140
  • Primary Citation of Related Structures:  
    1YED, 1YEC, 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 resol ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENT (D2.3)L219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENT (D2.3)H222Mus musculusMutation(s): 0 
Gene Names: Ighg
Find proteins for P01863 (Mus musculus)
Explore P01863 
Go to UniProtKB:  P01863
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNB
Query on PNB

Download CCD File 
H
4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
C13 H17 N2 O8 P
LNMNPGKCSJFAGN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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