1AXS

MATURE OXY-COPE CATALYTIC ANTIBODY WITH HAPTEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/38470

  • 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 cataly ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OXY-COPE CATALYTIC ANTIBODY
L, A
211Homo sapiensN/A
Find proteins for Q7Z3Y4 (Homo sapiens)
Go to UniProtKB:  Q7Z3Y4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
OXY-COPE CATALYTIC ANTIBODY
H, B
221Homo sapiensGene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HOP
Query on HOP

Download SDF File 
Download CCD File 
B, H
(1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL
OXY-COPE-HAPTEN
C23 H27 N O4
OBWILOKKNDYPLX-HBMCJLEFSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, H, L
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HOPKd: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.780α = 90.00
b = 81.500β = 93.43
c = 128.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-02-04
    Type: Initial release
  • Version 1.1: 2008-03-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance