1OAR

Fv IgE SPE-7 in complex with Alizarin Red


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibody Multispecificity Mediated by Conformational Diversity

James, L.C.Roversi, P.Tawfik, D.

(2003) Science 299: 1362

  • DOI: 10.1126/science.1079731
  • Primary Citation of Related Structures:  1OAQ, 1OAU, 1OAX, 1OAY, 1OAZ, 1OCW

  • PubMed Abstract: 
  • A single antibody was shown to adopt different binding-site conformations and thereby bind unrelated antigens. Analysis by both x-ray crystallography and pre-steady-state kinetics revealed an equilibrium between different preexisting isomers, one of ...

    A single antibody was shown to adopt different binding-site conformations and thereby bind unrelated antigens. Analysis by both x-ray crystallography and pre-steady-state kinetics revealed an equilibrium between different preexisting isomers, one of which possessed a promiscuous, low-affinity binding site for aromatic ligands, including the immunizing hapten. A subsequent induced-fit isomerization led to high-affinity complexes with a deep and narrow binding site. A protein antigen identified by repertoire selection made use of an unrelated antibody isomer with a wide, shallow binding site. Conformational diversity, whereby one sequence adopts multiple structures and multiple functions, can increase the effective size of the antibody repertoire but may also lead to autoimmunity and allergy.


    Organizational Affiliation

    Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2HQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN E
H, I, J, K
122Mus musculusGene Names: Ighv1-72 (Gm16709)
Find proteins for P01751 (Mus musculus)
Go to UniProtKB:  P01751
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULING E
L, M, N, O
110Mus musculusN/A
Find proteins for P01724 (Mus musculus)
Go to UniProtKB:  P01724
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
H, I, J, L, M, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
J, L, M, N, O
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AZN
Query on AZN

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Download CCD File 
H, I, J, K
ALIZARIN RED
C14 H8 O7 S
JKYKXTRKURYNGW-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
H, J
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
H, J, L, N
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

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Download CCD File 
H, J
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZNKd: 40 nM BINDINGMOAD
AZNKd: 40 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.917α = 90.00
b = 78.882β = 90.00
c = 169.036γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-15
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Derived calculations, Other, Source and taxonomy, Version format compliance