1YUH

FAB FRAGMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody.

Yuhasz, S.C.Parry, C.Strand, M.Amzel, L.M.

(1995) Mol.Immunol. 32: 1143-1155


  • PubMed Abstract: 
  • Affinity maturation of the immune response to nitrophenol-containing antigens has been extensively investigated. Significant strides made during the past several years with the advent of PCR technology have provided a wealth of biochemical knowledge. ...

    Affinity maturation of the immune response to nitrophenol-containing antigens has been extensively investigated. Significant strides made during the past several years with the advent of PCR technology have provided a wealth of biochemical knowledge. Structural investigations of the phenomena have however been limited. We have determined the three-dimensional structure of the Fab fragment of 88C6/12, an anti-4-hydroxy-3-nitrophenyl acetic acid antibody complexed with the immunizing hapten and with a heteroclitic iodinated hapten. The crystallographic structure of the complexes reveals that the binding is stabilized by a number of hydrogen bonds and extensive van der Waals interactions between the hapten and the antibody. In addition, the Fab binding pocket contains a region of positive electrostatic potential well suited for interaction with the predominant resonance form of the nitrophenyl ring system. The observed heteroclicity towards the iodinated hapten is not a direct result of iodine-protein interactions, but results from the enhanced stability in the iodinated ring of the resonance form that binds the antibody. In addition this investigation provides a rationale for the strong preference for the substitution in the heavy chain from the germ-line gene encoded Trp 33 to Leu 33 in the mature anti-nitrophenol response.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of an Anti-4-Hydroxy-3-Nitrophenylacetic Acid Monoclonal Antibody Fab Fragment Complexed with Immunizing and Heteroclitic Haptens
      Yuhasz, S.C.,Ysern, X.,Strand, M.,Amzel, L.M.
      (1989) J.Mol.Biol. 209: 319


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
88C6/12 FAB (LIGHT CHAIN)
L, A
211N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
88C6/12 FAB (HEAVY CHAIN)
H, B
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
NP
Query on NP

Download SDF File 
Download CCD File 
B, H
4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID
C14 H18 N2 O6
XAYGJFACOIKJCT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.200α = 90.00
b = 86.900β = 90.00
c = 131.100γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
X-PLORrefinement
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-09-18
    Type: Source and taxonomy
  • Version 1.4: 2018-03-21
    Type: Data collection, Other