1JGL

Crystal structure of immunoglobulin Fab fragment complexed with 17-beta-estradiol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a recombinant anti-estradiol Fab fragment in complex with 17beta -estradiol.

Lamminmaki, U.Kankare, J.A.

(2001) J.Biol.Chem. 276: 36687-36694

  • DOI: 10.1074/jbc.M102367200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of a Fab fragment of an anti-17beta-estradiol antibody 57-2 was determined in the absence and presence of the steroid ligand, 17beta-estradiol (E2), at 2.5 and 2.15-A resolutions, respectively. The antibody binds the steroid in ...

    The crystal structure of a Fab fragment of an anti-17beta-estradiol antibody 57-2 was determined in the absence and presence of the steroid ligand, 17beta-estradiol (E2), at 2.5 and 2.15-A resolutions, respectively. The antibody binds the steroid in a deep hydrophobic pocket formed at the interface between the variable domains. No major structural rearrangements take place upon ligand binding; however, a large part of the heavy chain variable domain near the binding pocket is unusually flexible and is partly stabilized when the steroid is bound. The nonpolar steroid skeleton of E2 is recognized by a number of hydrophobic interactions, whereas the two hydroxyl groups of E2 are hydrogen-bonded to the protein. Especially, the 17-hydroxyl group of E2 is recognized by an intricate hydrogen bonding network in which the 17-hydroxyl itself forms a rare four-center hydrogen bond with three polar amino acids; this hydrogen bonding arrangement accounts for the low cross-reactivity of the antibody with other estrogens such as estrone. The CDRH3 loop plays a prominent role in ligand binding. All the complementarity-determining regions of the light chain make direct contacts with the steroid, even CDRL2, which is rarely directly involved in the binding of haptens.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of a recombinant Fab fragment in complex with 17-beta-estradiol
      Lamminmaki, U.,Kankare, J.A.
      (2000) Acta Crystallogr.,Sect.D 56: 1670


    Organizational Affiliation

    Department of Biotechnology, University of Turku, Tykistökatu 6, 6th floor, 20520 Turku, Finland. urpo.lamminmaki@utu.fi




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig kappa-chain
L
214Mus musculusMutation(s): 0 
Find proteins for Q7TS98 (Mus musculus)
Go to UniProtKB:  Q7TS98
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ig gamma-1-chain
H
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EST
Query on EST

Download SDF File 
Download CCD File 
L
ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ESTKd: 2 nM BINDINGMOAD
ESTKd: 2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.207α = 90.00
b = 64.496β = 90.00
c = 165.285γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance