9IIE | pdb_00009iie

Cryogenic Temperature Crystal Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap

• PDB DOI: https://doi.org/10.2210/pdb9IIE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2024-06-20 Released: 2024-08-07 
• Deposition Author(s): Destan, E., DeMirci, H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 
  0.309 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap

Destan, E., Turkut, E., Aldeniz, A., Kang, J., Tosha, T., Yabashi, M., Yilmaz, B., Timucin, C., Matsuura, H., Kawano, Y., Cinkaya, I., Demirci, H.

(2025) Small Struct 

• DOI: https://doi.org/10.1002/sstr.202400680

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 50.15 kDa 
• Atom Count: 3,543 
• Modeled Residue Count: 414 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain	A, B	208	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	9		N-Glycosylation

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G45889JQ GlyCosmos: G45889JQ GlyGen: G45889JQ

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free:  0.309 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.92	α = 90
b = 80.48	β = 90
c = 137.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Destan, E., DeMirci, H.

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Funding Organization	Location	Grant Number
Other government	Turkey	--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2025-05-21
  Changes: Database references