1BM3

IMMUNOGLOBULIN OPG2 FAB-PEPTIDE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Conformational change in an anti-integrin antibody: structure of OPG2 Fab bound to a beta 3 peptide.

Kodandapani, R.Veerapandian, L.Ni, C.Z.Chiou, C.K.Whittal, R.M.Kunicki, T.J.Ely, K.R.

(1998) Biochem Biophys Res Commun 251: 61-66

  • DOI: https://doi.org/10.1006/bbrc.1998.9380
  • Primary Citation of Related Structures:  
    1BM3

  • PubMed Abstract: 

    Antibodies are important tools to explore receptor-ligand interactions. The anti-integrin antibody OPG2 binds in an RGD-related manner to the alphaIIb beta3 integrin as a molecular mimic of fibrinogen. The Fab fragment from OPG2 was cocrystallized with a peptide from the beta3 subunit of the integrin representing a site that binds RGD. The crystal structure of the complex was determined at 2.2-A resolution and compared with the unbound Fab. On binding the integrin peptide there were conformational changes in CDR3 of the heavy chain. Also, a significant shift across the intermolecular interface between the CH1-CL domains was observed so that the angle of rotation relating the two domains was reduced by 15 degrees. This unusual conformational adjustment represents the first example of ligand-induced conformational changes in the carboxyl domains of a Fab fragment.


  • Organizational Affiliation

    Cancer Research Center, The Burnham Institute, La Jolla, California, 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAINA [auth L]214Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAINB [auth H]227Mus musculusMutation(s): 0 
UniProt
Find proteins for P01868 (Mus musculus)
Explore P01868 
Go to UniProtKB:  P01868
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01868
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.152 
  • Space Group: A 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.11α = 90
b = 90.05β = 115.3
c = 79.11γ = 90
Software Package:
Software NamePurpose
UCSD-systemdata collection
NILSENdata reduction
X-PLORrefinement
UCSD-systemdata reduction
X-GENdata scaling
NILSENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-20
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-11-27
    Changes: Database references
  • Version 1.5: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description