Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Dihedral - D4  (3D View)
Pseudo Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 25.30 kDa 
• Atom Count: 1782 
• Modelled Residue Count: 230 
• Deposited Residue Count: 230 
• Unique protein chains: 2

2BJM

SPE7:Anthrone Complex

• PDB DOI: 10.2210/pdb2BJM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-04 Released: 2005-08-18 
• Deposition Author(s): James, L.C., Tawfik, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.286 
• R-Value Work: 0.268 
• R-Value Observed: 0.269 

Literature

Structure and Kinetics of a Transient Antibody Binding Intermediate Reveal a Kinetic Discrimination Mechanism in Antigen Recognition

James, L.C., Tawfik, D.S.

(2005) Proc Natl Acad Sci U S A 102: 12730

• PubMed: 16129832 
• DOI: 10.1073/pnas.0500909102
• Primary Citation of Related Structures:  
  2BJM


• PubMed Abstract: 
  

Induced fit is a predominant phenomenon in protein-ligand interactions, yet it is invariably attributed without establishing the existence, let alone the structure, of the initial, low-affinity encounter complex. We determined the crystal structure of the encounter complex on the pathway of ligand binding by IgE antibody SPE7. We show that this complex is formed by a wide range of ligands that initially bind with identical affinity. Nonspecific ligands rapidly dissociate, whereupon the antibody isomerizes to a nonbinding isomer. Specific ligand complexes, however, slowly isomerize to give a high-affinity complex. This isomerization involves backbone and side-chain rearrangements of up to 14 A and the formation of specific hydrogen bonds. The postbinding conformational switch, combined with the prebinding isomerization to an energetically favorable nonbinding isomer, results in a "kinetic discrimination" mechanism that mediates selective binding, by a factor of >10(3), between highly related ligands that initially bind with the same affinity. This model may apply to proteins that bind multiple ligands in a specific manner or other proteins that, although capable of binding many ligands, are activated by only a few.

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Organizational Affiliation: 

Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 2HQ, United Kingdom. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGE SPE7 HEAVY CHAIN	A [auth H]	120	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGE SPE7 LIGHT CHAIN	B [auth L]	110	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01724 (Mus musculus) Explore P01724  Go to UniProtKB:  P01724

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANF	C [auth H]	ANTHRONE C14 H10 O AUKRYONWZHRJRE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ANF	PDBBind:  2BJM	Kd: 2.00e+5 (nM) from 1 assay(s)
	Binding MOAD:  2BJM	Ka: 1.00e+5 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.286 
• R-Value Work: 0.268 
• R-Value Observed: 0.269 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.672	α = 90
b = 79.672	β = 90
c = 67.958	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-04 
• Released Date: 2005-08-18 
Deposition Author(s): James, L.C., Tawfik, D.S.

Revision History  

• Version 1.0: 2005-08-18
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance