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)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.68 kDa 
• Atom Count: 7342 
• Residue Count: 862 
• Unique protein chains: 2

2PCP

ANTIBODY FAB COMPLEXED WITH PHENCYCLIDINE

• DOI: 10.2210/pdb2PCP/pdb

• Classification: IMMUNOGLOBULIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1998-06-02 Released: 1999-01-27 
• Deposition Author(s): Lim, K., Owens, S.M., Arnold, L., Sacchettini, J.C., Linthicum, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.290 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Crystal structure of monoclonal 6B5 Fab complexed with phencyclidine.

Lim, K., Owens, S.M., Arnold, L., Sacchettini, J.C., Linthicum, D.S.

(1998) J Biol Chem 273: 28576-28582

• PubMed: 9786848 
• DOI: 10.1074/jbc.273.44.28576
• Primary Citation of Related Structures:  
  2PCP


• PubMed Abstract: 
  

The crystal structure of monoclonal antibody (mAb) 6B5 Fab fragment complexed with 1-(1-phenylcyclohexyl)piperidine (PCP or phencyclidine) was determined at 2.2-A resolution. 6B5 was originally produced from a mouse immunized with a phencyclidine analogue hapten 5-[N-(1'phenylcyclohexyl)amino]pentanoic acid conjugated to bovine serum albumin. This mAb was selected for further study because of its high affinity (Kd = 2 x 10(-9) M/liter) for PCP and usefulness in reversing PCP-induced central nervous system toxicity in laboratory animals. The dominant feature of the 6B5 Fab.PCP complex is the deep binding site and hydrophobic nature of the interaction. The ligand binding pocket of 6B5 Fab has numerous aromatic side chains, as compared with other known Fab structures. The most notable feature of the binding site is a Trp at position 97H (H-chain), and the side chain of this residue appears to act as a hydrophobic umbrella on the ligand in the antigen binding pocket. There are only two other known Fabs found with a Trp at the 97H position in complementarity determining region (CDR) H3, but they do not play a major role in the interaction with their respective antigens; in both Fab TE33 and R6.5 the Trp 97H side chain is positioned away from the bound antigen. Comparison of the CDR residues of 6B5 with other Fab structures with similar CDR sizes and amino acid compositions reveals a number of important patterns of residue substitutions that appear to be critical for specific PCP ligand interactions.

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Organizational Affiliation: 

Center for Structural Biology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN	A, C	216	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN	B, D	215	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PC	B, C	1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE C17 H25 N JTJMJGYZQZDUJJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1PC	Kd:  2   nM  Binding MOAD
1PC	Kd :  2   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.290 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.46	α = 62.11
b = 67.72	β = 84.66
c = 68.04	γ = 83.17

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-02 
• Released Date: 1999-01-27 
Deposition Author(s): Lim, K., Owens, S.M., Arnold, L., Sacchettini, J.C., Linthicum, D.S.

Revision History 

• Version 1.0: 1999-01-27
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance