5DK0

Fc Heterodimer Design 20.8.34 Y349S/T366M/K370Y/K409V + E356G/E357D/S364Q/Y407A

• PDB DOI: https://doi.org/10.2210/pdb5DK0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-09-02 Released: 2016-03-30 
• Deposition Author(s): Atwell, S., Leaver-Fay, A., Froning, K.J., Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R., Dhanani, S.H., Chamberlain, A.K., Fitchett, J.R., Gutierrez, B., Hendle, J., Demarest, S.J., Kuhlman, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.79 kDa 
• Atom Count: 3,566 
• Modelled Residue Count: 426 
• Deposited Residue Count: 480 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A	227	Homo sapiens	Mutation(s): 6  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	B	240	Homo sapiens	Mutation(s): 8  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fc-III peptide	C	13	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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	D, E	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G61334IA GlyCosmos:  G61334IA GlyGen:  G61334IA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.935	α = 90
b = 60.289	β = 103.2
c = 68.231	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Atwell, S., Leaver-Fay, A., Froning, K.J., Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R., Dhanani, S.H., Chamberlain, A.K., Fitchett, J.R., Gutierrez, B., Hendle, J., Demarest, S.J., Kuhlman, B.

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary