1OAR

Fv IgE SPE-7 in complex with Alizarin Red

PDB DOI: https://doi.org/10.2210/pdb1OAR/pdb

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

Deposited: 2003-01-21 Released: 2004-01-15
Deposition Author(s): James, L.C., Roversi, P., Tawfik, D.

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 1.2 of the entry. See complete history.

Literature

Antibody Multispecificity Mediated by Conformational Diversity

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

(2003) Science 299: 1362

PubMed: 12610298 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 104.85 kDa
Atom Count: 7,050
Modelled Residue Count: 839
Deposited Residue Count: 928
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN E	A [auth H], B [auth I], C [auth J], D [auth K]	122	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULING E	E [auth L], F [auth M], G [auth N], H [auth O]	110	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01724 (Mus musculus) Explore P01724 Go to UniProtKB: P01724
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01724
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZN Query on AZN Download Ideal Coordinates CCD File SDF format, chain EA [auth J] SDF format, chain HA [auth K] SDF format, chain R [auth H] SDF format, chain T [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain HA [auth K] MOL2 format, chain R [auth H] MOL2 format, chain T [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain HA [auth K] mmCIF format, chain R [auth H] mmCIF format, chain T [auth I]	EA [auth J], HA [auth K], R [auth H], T [auth I]	ALIZARIN RED C₁₄ H₈ O₇ S JKYKXTRKURYNGW-UHFFFAOYSA-N		Interactions Focus chain EA [auth J] Focus chain HA [auth K] Focus chain R [auth H] Focus chain T [auth I] Interactions & Density Focus chain EA [auth J] Focus chain HA [auth K] Focus chain R [auth H] Focus chain T [auth I]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain V [auth J] MOL2 format, chain I [auth H] MOL2 format, chain V [auth J] mmCIF format, chain I [auth H] mmCIF format, chain V [auth J]	I [auth H], V [auth J]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain I [auth H] Focus chain V [auth J] Interactions & Density Focus chain I [auth H] Focus chain V [auth J]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth J] SDF format, chain CA [auth J] SDF format, chain IA [auth L] SDF format, chain J [auth H] SDF format, chain JA [auth L] SDF format, chain K [auth H] SDF format, chain KA [auth L] SDF format, chain L [auth H] SDF format, chain LA [auth L] SDF format, chain M [auth H] SDF format, chain MA [auth L] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain TA [auth N] SDF format, chain UA [auth N] SDF format, chain VA [auth N] SDF format, chain W [auth J] SDF format, chain WA [auth N] SDF format, chain X [auth J] SDF format, chain XA [auth N] SDF format, chain Y [auth J] SDF format, chain Z [auth J] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain IA [auth L] MOL2 format, chain J [auth H] MOL2 format, chain JA [auth L] MOL2 format, chain K [auth H] MOL2 format, chain KA [auth L] MOL2 format, chain L [auth H] MOL2 format, chain LA [auth L] MOL2 format, chain M [auth H] MOL2 format, chain MA [auth L] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain TA [auth N] MOL2 format, chain UA [auth N] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth J] MOL2 format, chain WA [auth N] MOL2 format, chain X [auth J] MOL2 format, chain XA [auth N] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth J] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain IA [auth L] mmCIF format, chain J [auth H] mmCIF format, chain JA [auth L] mmCIF format, chain K [auth H] mmCIF format, chain KA [auth L] mmCIF format, chain L [auth H] mmCIF format, chain LA [auth L] mmCIF format, chain M [auth H] mmCIF format, chain MA [auth L] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain TA [auth N] mmCIF format, chain UA [auth N] mmCIF format, chain VA [auth N] mmCIF format, chain W [auth J] mmCIF format, chain WA [auth N] mmCIF format, chain X [auth J] mmCIF format, chain XA [auth N] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth J]	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		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain CA [auth J] Focus chain IA [auth L] Focus chain J [auth H] Focus chain JA [auth L] Focus chain K [auth H] Focus chain KA [auth L] Focus chain L [auth H] Focus chain LA [auth L] Focus chain M [auth H] Focus chain MA [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain TA [auth N] Focus chain UA [auth N] Focus chain VA [auth N] Focus chain W [auth J] Focus chain WA [auth N] Focus chain X [auth J] Focus chain XA [auth N] Focus chain Y [auth J] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain CA [auth J] Focus chain IA [auth L] Focus chain J [auth H] Focus chain JA [auth L] Focus chain K [auth H] Focus chain KA [auth L] Focus chain L [auth H] Focus chain LA [auth L] Focus chain M [auth H] Focus chain MA [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain TA [auth N] Focus chain UA [auth N] Focus chain VA [auth N] Focus chain W [auth J] Focus chain WA [auth N] Focus chain X [auth J] Focus chain XA [auth N] Focus chain Y [auth J] Focus chain Z [auth J]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth J] SDF format, chain Q [auth H] MOL2 format, chain DA [auth J] MOL2 format, chain Q [auth H] mmCIF format, chain DA [auth J] mmCIF format, chain Q [auth H]	DA [auth J], Q [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth J] Focus chain Q [auth H] Interactions & Density Focus chain DA [auth J] Focus chain Q [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth N] SDF format, chain BB [auth O] SDF format, chain GA [auth J] SDF format, chain OA [auth L] SDF format, chain PA [auth L] SDF format, chain QA [auth L] SDF format, chain SA [auth M] SDF format, chain ZA [auth N] MOL2 format, chain AB [auth N] MOL2 format, chain BB [auth O] MOL2 format, chain GA [auth J] MOL2 format, chain OA [auth L] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth L] MOL2 format, chain SA [auth M] MOL2 format, chain ZA [auth N] mmCIF format, chain AB [auth N] mmCIF format, chain BB [auth O] mmCIF format, chain GA [auth J] mmCIF format, chain OA [auth L] mmCIF format, chain PA [auth L] mmCIF format, chain QA [auth L] mmCIF format, chain SA [auth M] mmCIF format, chain ZA [auth N]	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		Interactions Focus chain AB [auth N] Focus chain BB [auth O] Focus chain GA [auth J] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain ZA [auth N] Interactions & Density Focus chain AB [auth N] Focus chain BB [auth O] Focus chain GA [auth J] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain SA [auth M] Focus chain ZA [auth N]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain FA [auth J] SDF format, chain NA [auth L] SDF format, chain RA [auth M] SDF format, chain S [auth H] SDF format, chain U [auth I] SDF format, chain YA [auth N] MOL2 format, chain FA [auth J] MOL2 format, chain NA [auth L] MOL2 format, chain RA [auth M] MOL2 format, chain S [auth H] MOL2 format, chain U [auth I] MOL2 format, chain YA [auth N] mmCIF format, chain FA [auth J] mmCIF format, chain NA [auth L] mmCIF format, chain RA [auth M] mmCIF format, chain S [auth H] mmCIF format, chain U [auth I] mmCIF format, chain YA [auth N]	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		Interactions Focus chain FA [auth J] Focus chain NA [auth L] Focus chain RA [auth M] Focus chain S [auth H] Focus chain U [auth I] Focus chain YA [auth N] Interactions & Density Focus chain FA [auth J] Focus chain NA [auth L] Focus chain RA [auth M] Focus chain S [auth H] Focus chain U [auth I] Focus chain YA [auth N]

Binding Affinity Annotations
ID	Source	Binding Affinity
AZN	PDBBind: 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 = 78.917	α = 90
b = 78.882	β = 90
c = 169.036	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-01-15

Deposition Author(s):

James, L.C.

Roversi, P.

Tawfik, D.

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
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Other, Structure summary