1GAF

48G7 HYBRIDOMA LINE FAB COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1086-1091


  • PubMed Abstract: 
  • The germline genes used by the mouse to generate the esterolytic antibody 48G7 were cloned and expressed in an effort to increase our understanding of the detailed molecular mechanisms by which the immune system evolves catalytic function. The nine r ...

    The germline genes used by the mouse to generate the esterolytic antibody 48G7 were cloned and expressed in an effort to increase our understanding of the detailed molecular mechanisms by which the immune system evolves catalytic function. The nine replacement mutations that were fixed during affinity maturation increased affinity for the transition state analogue by a factor of 10(4), primarily the result of a decrease in the dissociation rate of the hapten-antibody complex. There was a corresponding increase in the rate of reaction of antibody with substrate, k(cat)/k(m), from 1.7 x 10(2)M(-1) min(-1) to 1.4 x 10(4)M(-1) min(-1). The three-dimensional crystal structure of the 48G7-transition state analogue complex at 2.0 angstroms resolution indicates that one of the nine residues in which somatic mutations have been fixed directly contact the hapten. Thus, in the case of 48G7, affinity maturation appears to play a conformational role, either in reorganizing the active site geometry of limiting side-chain and backbone flexibility of the germline antibody. The crystal structure and analysis of somatic and directed active site mutants underscore the role of transition state stabilization in the evolution of this catalytic antibody.


    Related Citations: 
    • 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.USA 90: 1160


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHIMERIC 48G7 FAB
L
214Homo sapiensGene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Go to UniProtKB:  P01834
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CHIMERIC 48G7 FAB
H
217Homo sapiensGene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPE
Query on NPE

Download SDF File 
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: 10 nM BINDINGMOAD
NPEKd: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 140.260α = 90.00
b = 44.850β = 121.55
c = 85.450γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
DENZOdata reduction

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: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance