Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.66 kDa 
• Atom Count: 3810 
• Residue Count: 438 
• Unique protein chains: 2

1Q72

Anti-Cocaine Antibody M82G2 Complexed with Cocaine

• DOI: 10.2210/pdb1Q72/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2003-08-15 Released: 2003-08-26 
• Deposition Author(s): Pozharski, E., Moulin, A., Hewagama, A., Shanafelt, A.B., Petsko, G.A., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

Diversity in hapten recognition: structural study of an anti-cocaine antibody M82G2.

Pozharski, E., Moulin, A., Hewagama, A., Shanafelt, A.B., Petsko, G.A., Ringe, D.

(2005) J Mol Biol 349: 570-582

• PubMed: 15885702 
• DOI: 10.1016/j.jmb.2005.03.080
• Primary Citation of Related Structures:  
  1Q72, 1QYG, 1RFD


• PubMed Abstract: 
  

Antibodies against cocaine and other drugs of abuse are the basis for diagnostic tests for the presence of those drugs in human serum. The 1.7A resolution crystal structure of the anti-cocaine monoclonal antibody M82G2 in complex with cocaine is presented. This structure determination was undertaken to establish the stereochemical features in the antibody binding site that confer specificity for cocaine, and as part of an ongoing project to understand the rules that govern molecular recognition. The cocaine-binding site can be characterized topologically as a narrow groove on the protein surface. The antibody utilizes water-mediated hydrogen bonding, and cation-pi and stacking (pi-pi) interactions to provide specificity. Comparison with the previously published structure of the anti-cocaine antibody GNC92H2 shows that binding of a small ligand can be achieved in diverse ways, both in terms of a binding site structure/topology and protein-ligand interactions.

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Organizational Affiliation: 

Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab M82G2, Light chain	L	218	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab M82G2, Heavy chain	H	223	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COC	H	COCAINE C17 H21 N O4 ZPUCINDJVBIVPJ-LJISPDSOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
COC	Kd:  1450   nM  Binding MOAD
COC	Kd :  140   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.386	α = 90
b = 75.386	β = 90
c = 150.817	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-15 
• Released Date: 2003-08-26 
Deposition Author(s): Pozharski, E., Moulin, A., Hewagama, A., Shanafelt, A.B., Petsko, G.A., Ringe, D.

Revision History 

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance