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


Ligand Structure Quality Assessment 


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: https://doi.org/10.1126/science.1079731
  • Primary Citation of Related Structures:  
    1OAQ, 1OAR, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN EA [auth H],
B [auth I],
C [auth J],
D [auth K]
122Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULING EE [auth L],
F [auth M],
G [auth N],
H [auth O]
110Mus musculusMutation(s): 0 
UniProt
Find proteins for P01724 (Mus musculus)
Explore P01724 
Go to UniProtKB:  P01724
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01724
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AZN
Query on AZN

Download Ideal Coordinates CCD File 
EA [auth J],
HA [auth K],
R [auth H],
T [auth I]
ALIZARIN RED
C14 H8 O7 S
JKYKXTRKURYNGW-UHFFFAOYSA-N
CAC
Query on CAC

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I [auth H],
V [auth J]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
DMS
Query on DMS

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AA [auth J]
BA [auth J]
CA [auth J]
IA [auth L]
J [auth H]
AA [auth J],
BA [auth J],
CA [auth J],
IA [auth L],
J [auth H],
JA [auth L],
K [auth H],
KA [auth L],
L [auth H],
LA [auth L],
M [auth H],
MA [auth L],
N [auth H],
O [auth H],
P [auth H],
TA [auth N],
UA [auth N],
VA [auth N],
W [auth J],
WA [auth N],
X [auth J],
XA [auth N],
Y [auth J],
Z [auth J]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

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DA [auth J],
Q [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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AB [auth N]
BB [auth O]
GA [auth J]
OA [auth L]
PA [auth L]
AB [auth N],
BB [auth O],
GA [auth J],
OA [auth L],
PA [auth L],
QA [auth L],
SA [auth M],
ZA [auth N]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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FA [auth J]
NA [auth L]
RA [auth M]
S [auth H]
U [auth I]
FA [auth J],
NA [auth L],
RA [auth M],
S [auth H],
U [auth I],
YA [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AZN PDBBind:  1OAR Kd: 40 (nM) from 1 assay(s)
Binding MOAD:  1OAR Kd: 40 (nM) from 1 assay(s)
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
b = 78.882β = 90
c = 169.036γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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