1AJ7

IMMUNOGLOBULIN 48G7 GERMLINE FAB ANTIBODY COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID. AFFINITY MATURATION OF AN ESTEROLYTIC ANTIBODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the evolution of an antibody combining site.

Wedemayer, G.J.Patten, P.A.Wang, L.H.Schultz, P.G.Stevens, R.C.

(1997) Science 276: 1665-1669

  • DOI: 10.1126/science.276.5319.1665
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structures of a germline antibody Fab fragment and its complex with hapten have been solved at 2.1 A resolution. These structures are compared with the corresponding crystal structures of the affinity-matured antibody, 48G7, which has a 3 ...

    The crystal structures of a germline antibody Fab fragment and its complex with hapten have been solved at 2.1 A resolution. These structures are compared with the corresponding crystal structures of the affinity-matured antibody, 48G7, which has a 30,000 times higher affinity for hapten as a result of nine replacement somatic mutations. Significant changes in the configuration of the combining site occur upon binding of hapten to the germline antibody, whereas hapten binds to the mature antibody by a lock-and-key fit mechanism. The reorganization of the combining site that was nucleated by hapten binding is further optimized by somatic mutations that occur up to 15 from bound hapten. These results suggest that the binding potential of the primary antibody repertoire may be significantly expanded by the ability of germline antibodies to adopt more than one combining-site configuration, with both antigen binding and somatic mutation stabilizing the configuration with optimal hapten complementarity.


    Related Citations: 
    • Crystal Structures of the Free and Liganded Form of an Esterolytic Catalytic Antibody
      Wedemayer, G.J., Wang, L.H., Patten, P.A., Schultz, P.G., Stevens, R.C.
      (1997) J Mol Biol 268: 390
    • The Immunological Evolution of Catalysis
      Patten, P.A., Gray, N.S., Yang, P.L., Marks, C.B., Wedemayer, G.J., Boniface, J.J., Stevens, R.C., Schultz, P.G.
      (1996) Science 271: 1086
    • A Genetic Approach to the Generation of Antibodies with Enhanced Catalytic Activities
      Lesley, S.A., Patten, P.A., Schultz, P.G.
      (1993) Proc Natl Acad Sci U S A 90: 1160

    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, CA 94720, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN 48G7 FAB (LIGHT CHAIN)L214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN 48G7 FAB (HEAVY CHAIN)H217Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS  P01857
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPE
Query on NPE

Download CCD File 
H
5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID
C11 H13 N O7 P
XVVZSEXTAACTPS-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NPEKd :  135000   nM  PDBBind
NPEKd:  135000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.1α = 90
b = 60.9β = 104.8
c = 73.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance