1VFB

BOUND WATER MOLECULES AND CONFORMATIONAL STABILIZATION HELP MEDIATE AN ANTIGEN-ANTIBODY ASSOCIATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bound water molecules and conformational stabilization help mediate an antigen-antibody association.

Bhat, T.N.Bentley, G.A.Boulot, G.Greene, M.I.Tello, D.Dall'Acqua, W.Souchon, H.Schwarz, F.P.Mariuzza, R.A.Poljak, R.J.

(1994) Proc.Natl.Acad.Sci.USA 91: 1089-1093

  • Primary Citation of Related Structures:  1VFA

  • PubMed Abstract: 
  • We report the three-dimensional structures, at 1.8-A resolution, of the Fv fragment of the anti-hen egg white lysozyme antibody D1.3 in its free and antigen-bound forms. These structures reveal a role for solvent molecules in stabilizing the complex ...

    We report the three-dimensional structures, at 1.8-A resolution, of the Fv fragment of the anti-hen egg white lysozyme antibody D1.3 in its free and antigen-bound forms. These structures reveal a role for solvent molecules in stabilizing the complex and provide a molecular basis for understanding the thermodynamic forces which drive the association reaction. Four water molecules are buried and others form a hydrogen-bonded network around the interface, bridging antigen and antibody. Comparison of the structures of free and bound Fv fragment of D1.3 reveals that several of the ordered water molecules in the free antibody combining site are retained and that additional water molecules link antigen and antibody upon complex formation. This solvation of the complex should weaken the hydrophobic effect, and the resulting large number of solvent-mediated hydrogen bonds, in conjunction with direct protein-protein interactions, should generate a significant enthalpic component. Furthermore, a stabilization of the relative mobilities of the antibody heavy- and light-chain variable domains and of that of the third complementarity-determining loop of the heavy chain seen in the complex should generate a negative entropic contribution opposing the enthalpic and the hydrophobic (solvent entropy) effects. This structural analysis is consistent with measurements of enthalpy and entropy changes by titration calorimetry, which show that enthalpy drives the antigen-antibody reaction. Thus, the main forces stabilizing the complex arise from antigen-antibody hydrogen bonding, van der Waals interactions, enthalpy of hydration, and conformational stabilization rather than solvent entropy (hydrophobic) effects.


    Related Citations: 
    • Small Rearrangements in Structures of Fv and Fab Fragments of an Antibody D1.3 On Antigen Binding
      Bhat, T.N.,Bentley, G.A.,Fischmann, T.O.,Boulot, G.,Poljak, R.J.
      (1990) Nature 347: 483


    Organizational Affiliation

    Centre National de la Recherche Scientifique, Unité Associée 359, Institut Pasteur, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA D1.3 FV (LIGHT CHAIN)
A
107Mus musculusN/A
Find proteins for P01635 (Mus musculus)
Go to UniProtKB:  P01635
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA D1.3 FV (HEAVY CHAIN)
B
116Mus musculusN/A
Find proteins for P01820 (Mus musculus)
Go to UniProtKB:  P01820
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HEN EGG WHITE LYSOZYME
C
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 129.200α = 90.00
b = 60.800β = 119.30
c = 56.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance