1AXS

MATURE OXY-COPE CATALYTIC ANTIBODY WITH HAPTEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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This is version 1.3 of the entry. See complete history


Literature

The interplay between binding energy and catalysis in the evolution of a catalytic antibody.

Ulrich, H.D.Mundorff, E.Santarsiero, B.D.Driggers, E.M.Stevens, R.C.Schultz, P.G.

(1997) Nature 389: 271-275

  • DOI: https://doi.org/10.1038/38470
  • Primary Citation of Related Structures:  
    1AXS

  • PubMed Abstract: 

    Antibody catalysis provides an opportunity to examine the evolution of binding energy and its relation to catalytic function in a system that has many parallels with natural enzymes. Here we report such a study involving an antibody AZ-28 that catalyses an oxy-Cope rearrangement, a pericyclic reaction that belongs to a well studied and widely used class of reactions in organic chemistry. Immunization with transition state analogue 1 results in a germline-encoded antibody that catalyses the rearrangement of hexadiene 2 to aldehyde 3 with a rate approaching that of a related pericyclic reaction catalysed by the enzyme chorismate mutase. Affinity maturation gives antibody AZ-28, which has six amino acid substitutions, one of which results in a decrease in catalytic rate. To understand the relationship between binding and catalytic rate in this system we characterized a series of active-site mutants and determined the three-dimensional crystal structure of the complex of AZ-28 with the transition state analogue. This analysis indicates that the activation energy depends on a complex balance of several stereoelectronic effects which are controlled by an extensive network of binding interactions in the active site. Thus in this instance the combinatorial diversity of the immune system provided both an efficient catalyst for a reaction where no enzyme is known, as well as an opportunity to explore the mechanisms and evolution of biological catalysis.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OXY-COPE CATALYTIC ANTIBODYA [auth L],
C [auth A]
211Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens)
Explore Q7Z3Y4 
Go to UniProtKB:  Q7Z3Y4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z3Y4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OXY-COPE CATALYTIC ANTIBODYB [auth H],
D [auth B]
221Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
PHAROS:  P01857
GTEx:  ENSG00000211896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01857
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HOP
Query on HOP

Download Ideal Coordinates CCD File 
J [auth H],
N [auth B]
(1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL
C23 H27 N O4
OBWILOKKNDYPLX-HBMCJLEFSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
E [auth L]
F [auth L]
G [auth L]
H
I [auth H]
E [auth L],
F [auth L],
G [auth L],
H,
I [auth H],
K [auth A],
L [auth A],
M [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
HOP PDBBind:  1AXS Kd: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.78α = 90
b = 81.5β = 93.43
c = 128.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-02-04
    Type: Initial release
  • Version 1.1: 2008-03-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description