5NSC

Fc DEKK heterodimer variant

• PDB DOI: https://doi.org/10.2210/pdb5NSC/pdb

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


• Deposited: 2017-04-26 Released: 2017-07-05 
• Deposition Author(s): De Nardis, C., Hendriks, L.J.A., Poirier, E., Arvinte, T., Gros, P., Bakker, A.B.H., de Kruif, J.
• Funding Organization(s): European Union Seventh Framework Programme (FP7/2007-2013)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.265 
• 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)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 56.8 kDa 
• Atom Count: 3,855 
• Modelled Residue Count: 432 
• Deposited Residue Count: 477 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein DKFZp686C11235	A	232	Homo sapiens	Mutation(s): 2  Gene Names: DKFZp686C11235
UniProt
Find proteins for Q6MZV7 (Homo sapiens) Explore Q6MZV7  Go to UniProtKB:  Q6MZV7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein DKFZp686C11235	B	232	Homo sapiens	Mutation(s): 5  Gene Names: DKFZp686C11235
UniProt
Find proteins for Q6MZV7 (Homo sapiens) Explore Q6MZV7  Go to UniProtKB:  Q6MZV7

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.265 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.059	α = 90
b = 65.442	β = 103.24
c = 78.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-05 
Deposition Author(s): De Nardis, C., Hendriks, L.J.A., Poirier, E., Arvinte, T., Gros, P., Bakker, A.B.H., de Kruif, J.

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Funding Organization	Location	Grant Number
European Union Seventh Framework Programme (FP7/2007-2013)	Netherlands	283570

Revision History  

• Version 1.0: 2017-07-05
  Type: Initial release
  
• Version 1.1: 2017-07-12
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary