1YEC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 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

  • Primary Citation of Related Structures:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A FAB FRAGMENT (D2.3)
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A FAB FRAGMENT (D2.3)
H
222Mus musculusMutation(s): 0 
Gene Names: Ighg
Find proteins for P01863 (Mus musculus)
Go to UniProtKB:  P01863
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PNB
Query on PNB

Download SDF File 
Download CCD File 
H
4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
C13 H17 N2 O8 P
LNMNPGKCSJFAGN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.180α = 90.00
b = 78.180β = 90.00
c = 158.940γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
CCP4data scaling
X-PLORrefinement
CCP4data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance