1D5B

UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement.

Mundorff, E.C.Hanson, M.A.Varvak, A.Ulrich, H.Schultz, P.G.Stevens, R.C.

(2000) Biochemistry 39: 627-632

  • DOI: 10.1021/bi9924314
  • Primary Citation of Related Structures:  
    1D5I, 1D5B, 1D6V

  • PubMed Abstract: 
  • Antibody AZ-28 was generated against the chairlike transition-state analogue (TSA) 1 and catalyzes the oxy-Cope rearrangement of substrate 2 to product 3. The germline precursor to AZ-28 catalyzes the reaction with a 35-fold higher rate (k(cat)/k(unc ...

    Antibody AZ-28 was generated against the chairlike transition-state analogue (TSA) 1 and catalyzes the oxy-Cope rearrangement of substrate 2 to product 3. The germline precursor to AZ-28 catalyzes the reaction with a 35-fold higher rate (k(cat)/k(uncat) = 163 000), despite a 40-fold lower binding affinity for TSA.1 (K(D) = 670 nM). To determine the structural basis for the differences in the binding and catalytic properties of the germline and affinity-matured antibodies, the X-ray crystal structures of the unliganded and TSA.1 complex of antibody AZ-28 have been determined at 2.8 and 2.6 A resolution, respectively; the structures of the unliganded and TSA.1 complex of the germline precursor to AZ-28 were both determined at 2. 0 A resolution. In the affinity-matured antibody.hapten complex the TSA is fixed in a catalytically unfavorable conformation by a combination of van der Waals and hydrogen-bonding interactions. The 2- and 5-phenyl substituents of TSA.1 are almost perpendicular to the cyclohexyl ring, leading to decreased orbital overlap and decreased stabilization of the putative transition state. The active site of the germline antibody appears to have an increased degree of flexibility-CDRH3 moves 4.9 A outward from the active site upon binding of TSA.1. We suggest that this conformational flexibility in the germline antibody, which results in a lower binding affinity for TSA.1, allows dynamic changes in the dihedral angle of the 2-phenyl substituent along the reaction coordinate. These conformational changes in turn lead to enhanced orbital overlap and increased catalytic rate. These studies suggest that protein and substrate dynamics play a key role in this antibody-catalyzed reaction.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
chimeric OXY-COPE catalytic ANTIBODY AZ-28 (light chain)AL211Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
NIH Common Fund Data Resources
PHAROS  P01834
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
chimeric OXY-COPE catalytic ANTIBODY AZ-28 (HEAVY chain)BH221Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
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
CD
Query on CD

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.42α = 90
b = 80.67β = 90
c = 134.75γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary