1F11

F124 FAB FRAGMENT FROM A MONOCLONAL ANTI-PRES2 ANTIBODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Fab fragment from F124, a monoclonal antibody specific for hepatitis B surface antigen.

Saul, F.A.Vulliez-Le Normand, B.Passafiume, M.Riottot, M.M.Bentley, G.A.

(2000) Acta Crystallogr.,Sect.D 56: 945-951


  • PubMed Abstract: 
  • The crystal structure of the Fab fragment from the monoclonal anti-preS2 antibody F124 (IgG1,kappa) has been solved by molecular replacement and refined at 3.0 A resolution. The Fab crystallizes with two independent molecules in the asymmetric unit. ...

    The crystal structure of the Fab fragment from the monoclonal anti-preS2 antibody F124 (IgG1,kappa) has been solved by molecular replacement and refined at 3.0 A resolution. The Fab crystallizes with two independent molecules in the asymmetric unit. F124 recognizes an epitope contained within the preS2 segment between residues 120 and 132 of the surface antigen of hepatitis B virus. The antibody shows a high affinity for the glycan N-linked to Asn123, but it also cross-reacts with the non-glycosylated peptide fragment 120-132. Although crystallization was performed in the presence of an eightfold excess of the cross-reactive peptide, no evidence for the ligand was found in the antigen-binding site, which is close to a neighbouring molecule in the crystal lattice. The antigen-binding site has a groove-like topology which is modulated with pocket-like cavities. It is characterized by a large number of tyrosine and aspartate residues. The importance of germ-line mutations at the binding site is discussed.


    Related Citations: 
    • Sequence Analysis of a Monoclonal Antibody Specific for the preS2 Region of Hepatitis B Surface Antigen, and the Cloning, Expression and Characterisation of its Single-chain Fv Construction
      Passafiume, M.,Vulliez-le Normand, B.,Riottot, M.M.,Bentley, G.A.
      (1998) FEBS Lett. 441: 407


    Organizational Affiliation

    Unité d'Immunologie Structurale, CNRS URA 2185, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
F124 IMMUNOGLOBULIN (KAPPA LIGHT CHAIN)
A, C
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
F124 IMMUNOGLOBULIN (IGG1 HEAVY CHAIN)
B, D
221Mus musculusMutation(s): 0 
Find proteins for Q9D8L4 (Mus musculus)
Go to UniProtKB:  Q9D8L4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.700α = 90.00
b = 54.000β = 101.00
c = 120.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-21
    Type: Database references, Source and taxonomy, Structure summary