2AK1

Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with benzoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Complete reaction cycle of a cocaine catalytic antibody at atomic resolution.

Zhu, X., Dickerson, T.J., Rogers, C.J., Kaufmann, G.F., Mee, J.M., McKenzie, K.M., Janda, K.D., Wilson, I.A.

(2006) Structure 14: 205-216

  • DOI: 10.1016/j.str.2005.10.014
  • Primary Citation of Related Structures:  
    2AK1, 2AJZ, 2AJY, 2AJX, 2AJV, 2AJU, 2AJS

  • PubMed Abstract: 

    • Antibody 7A1 hydrolyzes cocaine to produce nonpsychoactive metabolites ecgonine methyl ester and benzoic acid. Crystal structures of 7A1 Fab' and six complexes with substrate cocaine, the transition state analog, products ecgonine methyl ester and benzoi ...

    Antibody 7A1 hydrolyzes cocaine to produce nonpsychoactive metabolites ecgonine methyl ester and benzoic acid. Crystal structures of 7A1 Fab' and six complexes with substrate cocaine, the transition state analog, products ecgonine methyl ester and benzoic acid together and individually, as well as heptaethylene glycol have been analyzed at 1.5-2.3 angstroms resolution. Here, we present snapshots of the complete cycle of the cocaine hydrolytic reaction at atomic resolution. Significant structural rearrangements occur along the reaction pathway, but they are generally limited to the binding site, including the ligands themselves. Several interacting side chains either change their rotamers or alter their mobility to accommodate the different reaction steps. CDR loop movements (up to 2.3 angstroms) and substantial side chain rearrangements (up to 9 angstroms) alter the shape and size (approximately 320-500 angstroms3) of the antibody active site from "open" to "closed" to "open" for the substrate, transition state, and product states, respectively.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 7A1 Fab' L216Mus musculusMutation(s): 0 
Gene Names: Igkc
Find proteins for P01837 (Mus musculus)
Explore P01837 
Go to UniProtKB:  P01837
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 7A1 Fab' H219Mus musculusMutation(s): 0 
Find proteins for Q5M842 (Rattus norvegicus)
Explore Q5M842 
Go to UniProtKB:  Q5M842
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.217 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.595α = 90
b = 89.106β = 90
c = 153.454γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2005-08-02 
  • Released Date: 2006-02-14 
    • Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description