1JNN

Crystal Structure of Fab-Estradiol Complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Highly specific anti-estradiol antibodies: structural characterisation and binding diversity.

Monnet, C.Bettsworth, F.Stura, E.A.Du, M.H.Menez, R.Derrien, L.Zinn-Justin, S.Gilquin, B.Sibai, G.Battail-Poirot, N.Jolivet, M.Menez, A.Arnaud, M.Ducancel, F.Charbonnier, J.B.

(2002) J Mol Biol 315: 699-712

  • DOI: https://doi.org/10.1006/jmbi.2001.5284
  • Primary Citation of Related Structures:  
    1JN6, 1JNH, 1JNL, 1JNN

  • PubMed Abstract: 

    Subtle modulation of antibody-binding properties by protein engineering often lies with an accurate structural and energetic description of how an antigen is recognised. Thus, with the intent to increase the affinity and add a bias in favour of natural estradiol compared with its chemically modified immunogen, we have determined the crystal structure of two anti-estradiol monoclonal antibodies, 10G6D6 and 17E12E5. Although generated against the same estradiol derivative, these antibodies share little sequence identity, which is reflected in dissimilar binding pockets and in different positioning of the steroid. In both antibodies the characteristic 17-hydroxyl group is buried deeply at the bottom of hydrophobic pockets and stabilised by hydrogen bonds. Apart from this similarity, the steroid is oriented differently in the respective binding pockets. The high specificity of both antibodies has been mapped out, and even closely related steroids show low cross-reactivity. The structural studies of the complex formed between 10G6D6 and 6-CMO-estradiol have identified contacts between the 6-CMO coupling linker and an arginine residue from the heavy chain CDR2 segment. This segment is now being targeted by random mutagenesis to select mutants with a preference for natural estradiol compared to the branched hapten.


  • Organizational Affiliation

    Département d'Ingénierie et d'Etude des Protéines, CEA, CE Saclay, Gif-sur-Yvette Cedex, 91191, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MONOCLONAL ANTI-ESTRADIOL 17E12E5 IMMUNOGLOBULIN KAPPA CHAINA [auth L]211Mus musculusMutation(s): 0 
UniProt
Find proteins for Q7TS98 (Mus musculus)
Explore Q7TS98 
Go to UniProtKB:  Q7TS98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7TS98
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MONOCLONAL ANTI-ESTRADIOL 17E12E5 IMMUNOGLOBULIN GAMMA-1 CHAINB [auth H]214Mus musculusMutation(s): 0 
UniProt
Find proteins for Q99LC4 (Mus musculus)
Explore Q99LC4 
Go to UniProtKB:  Q99LC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99LC4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EST
Query on EST

Download Ideal Coordinates CCD File 
C [auth H]ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.95α = 90
b = 143.24β = 90
c = 53.37γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description