2AJS

Crystal structure of cocaine catalytic antibody 7A1 Fab' in complex with heptaethylene glycol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.209 

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:  2AJU, 2AJV, 2AJX, 2AJY, 2AJZ, 2AK1

  • 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 be ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody 7A1 FAB'
L
216Mus musculusN/A
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody 7A1 FAB'
H
219Rattus norvegicusGene Names: IgG-2a
Find proteins for Q5M842 (Rattus norvegicus)
Go to UniProtKB:  Q5M842
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download SDF File 
Download CCD File 
H
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
HEPTAETHYLENE GLYCOL, PEG330
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.209 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.107α = 90.00
b = 88.107β = 90.00
c = 135.397γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description