4LLY

Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns (VRD2 and CRD2) at 1.6A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report



Literature

Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface.

Lewis, S.M., Wu, X., Pustilnik, A., Sereno, A., Huang, F., Rick, H.L., Guntas, G., Leaver-Fay, A., Smith, E.M., Ho, C., Hansen-Estruch, C., Chamberlain, A.K., Truhlar, S.M., Conner, E.M., Atwell, S., Kuhlman, B., Demarest, S.J.

(2014) Nat Biotechnol 32: 191-198

  • DOI: 10.1038/nbt.2797
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Robust generation of IgG bispecific antibodies has been a long-standing challenge. Existing methods require extensive engineering of each individual antibody, discovery of common light chains, or complex and laborious biochemical processing. Here we ...

    Robust generation of IgG bispecific antibodies has been a long-standing challenge. Existing methods require extensive engineering of each individual antibody, discovery of common light chains, or complex and laborious biochemical processing. Here we combine computational and rational design approaches with experimental structural validation to generate antibody heavy and light chains with orthogonal Fab interfaces. Parental monoclonal antibodies incorporating these interfaces, when simultaneously co-expressed, assemble into bispecific IgG with improved heavy chain-light chain pairing. Bispecific IgGs generated with this approach exhibit pharmacokinetic and other desirable properties of native IgG, but bind target antigens monovalently. As such, these bispecific reagents may be useful in many biotechnological applications.

    Organizational Affiliation: 

    Eli Lilly Biotechnology Center, San Diego, California, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mutated Pertuzumab Fab heavy chainA, C226Homo sapiensMutation(s): 0 
Find proteins for S6B291 (Homo sapiens)
Explore S6B291 
Go to UniProtKB:  S6B291
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
light chain ClambdaB, D212Homo sapiensMutation(s): 0 
Gene Names: IGLC2
Find proteins for P0DOY2 (Homo sapiens)
Explore P0DOY2 
Go to UniProtKB:  P0DOY2
NIH Common Fund Data Resources
GTEx  ENSG00000211677
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.772α = 76.88
b = 52.847β = 84.32
c = 89.483γ = 85.53
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2014-03-26
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2019-06-26
    Changes: Advisory, Data collection, Database references, Polymer sequence, Source and taxonomy, Structure summary