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: 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 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
MoleculeChainsSequence 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / 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
 Ligand Interaction
CAC
Query on CAC

Download Ideal Coordinates CCD File 
I [auth H],
V [auth J]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth J],
Q [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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

View Full Validation Report



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