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: 1.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

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
  • Primary Citation of Related Structures:  

  • 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: 

    1] Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mutated Pertuzumab Fab heavy chain
A, C
226Homo sapiensMutation(s): 0 
Find proteins for S6B291 (Homo sapiens)
Go to UniProtKB:  S6B291
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
light chain Clambda
B, D
212Homo sapiensMutation(s): 0 
Gene Names: IGLC3
Find proteins for P0DOY3 (Homo sapiens)
Go to UniProtKB:  P0DOY3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • 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
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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