5DJ0

Fc Heterodimer Design 11.2 Y349S/K370Y + E357D/S364Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Computationally Designed Bispecific Antibodies using Negative State Repertoires.

Leaver-Fay, A.Froning, K.J.Atwell, S.Aldaz, H.Pustilnik, A.Lu, F.Huang, F.Yuan, R.Hassanali, S.Chamberlain, A.K.Fitchett, J.R.Demarest, S.J.Kuhlman, B.

(2016) Structure 24: 641-651

  • DOI: 10.1016/j.str.2016.02.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A challenge in the structure-based design of specificity is modeling the negative states, i.e., the complexes that you do not want to form. This is a difficult problem because mutations predicted to destabilize the negative state might be accommodate ...

    A challenge in the structure-based design of specificity is modeling the negative states, i.e., the complexes that you do not want to form. This is a difficult problem because mutations predicted to destabilize the negative state might be accommodated by small conformational rearrangements. To overcome this challenge, we employ an iterative strategy that cycles between sequence design and protein docking in order to build up an ensemble of alternative negative state conformations for use in specificity prediction. We have applied our technique to the design of heterodimeric CH3 interfaces in the Fc region of antibodies. Combining computationally and rationally designed mutations produced unique designs with heterodimer purities greater than 90%. Asymmetric Fc crystallization was able to resolve the interface mutations; the heterodimer structures confirmed that the interfaces formed as designed. With these CH3 mutations, and those made at the heavy-/light-chain interface, we demonstrate one-step synthesis of four fully IgG-bispecific antibodies.


    Organizational Affiliation

    Department of Biochemistry, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Campus Box 7260, Chapel Hill, NC 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig gamma-1 chain C region
A
227Homo sapiensMutation(s): 2 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ig gamma-1 chain C region
B
240Homo sapiensMutation(s): 5 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fc-III peptide
C
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.417α = 90.00
b = 67.340β = 104.70
c = 78.308γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references