Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.02 kDa 
• Atom Count: 7,945 
• Modelled Residue Count: 432 
• Deposited Residue Count: 464 
• Unique protein chains: 2

 4BSV

Heterodimeric Fc Antibody Azymetric Variant 1

• PDB DOI: 10.2210/pdb4BSV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2013-06-11 Released: 2013-08-21 
• Deposition Author(s): Suits, M.D.L., Spreter, T., Cabrera, E.E., Dixit, S.B., Lario, P.I., Poon, D.K.Y., D'Angelo, I.E.P., Boulanger, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.208 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

Improving Biophysical Properties of a Bispecific Antibody Scaffold to Aid Developability: Quality by Molecular Design.

Von Kreudenstein, T.S., Escobar-Carbrera, E., Lario, P.I., D'Angelo, I., Brault, K., Kelly, J., Durocher, Y., Baardsnes, J., Woods, R.J., Xie, M.H., Girod, P., Suits, M.D.L., Boulanger, M.J., Poon, D.K.Y., Ng, G.Y.K., Dixit, S.B.

(2013) MAbs 5: 646

• PubMed: 23924797 
• DOI: 10.4161/mabs.25632
• Primary Citation of Related Structures:  
  4BSV, 4BSW


• PubMed Abstract: 
  

While the concept of Quality-by-Design is addressed at the upstream and downstream process development stages, we questioned whether there are advantages to addressing the issues of biologics quality early in the design of the molecule based on fundamental biophysical characterization, and thereby reduce complexities in the product development stages. Although limited number of bispecific therapeutics are in clinic, these developments have been plagued with difficulty in producing materials of sufficient quality and quantity for both preclinical and clinical studies. The engineered heterodimeric Fc is an industry-wide favorite scaffold for the design of bispecific protein therapeutics because of its structural, and potentially pharmacokinetic, similarity to the natural antibody. Development of molecules based on this concept, however, is challenged by the presence of potential homodimer contamination and stability loss relative to the natural Fc. We engineered a heterodimeric Fc with high heterodimeric specificity that also retains natural Fc-like biophysical properties, and demonstrate here that use of engineered Fc domains that mirror the natural system translates into an efficient and robust upstream stable cell line selection process as a first step toward a more developable therapeutic.

---

Organizational Affiliation: 

Zymeworks Inc.; Vancouver, BC Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2	A	226	Homo sapiens	Mutation(s): 7  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2	B	226	Homo sapiens	Mutation(s): 7  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N/A
Glycosylation Resources
GlyTouCan:  G75031VE GlyCosmos:  G75031VE GlyGen:  G75031VE

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose	E	2		N/A
Glycosylation Resources
GlyTouCan:  G85856KC GlyCosmos:  G85856KC GlyGen:  G85856KC

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G27919IH GlyCosmos:  G27919IH GlyGen:  G27919IH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	P [auth B], Q [auth B], R [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.208 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.54	α = 90
b = 74.92	β = 90
c = 148.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Suits, M.D.L., Spreter, T., Cabrera, E.E., Dixit, S.B., Lario, P.I., Poon, D.K.Y., D'Angelo, I.E.P., Boulanger, M.J.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary