9BEX | pdb_00009bex

X-ray crystallography structural model of the immunoglobulin G1 (IgG1) Fc D270C K326C variant

• PDB DOI: https://doi.org/10.2210/pdb9BEX/pdb

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


• Deposited: 2024-04-16 Released: 2025-04-30 
• Deposition Author(s): Shenoy, A., Barb, A.W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.302 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.244 (DCC) 

Starting Model: experimental

Literature

X-ray crystallography structural model of the immunoglobulin G1 (IgG1) Fc D270C K326C variant

Shenoy, A., Barb, A.W.

To be published.

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.53 kDa 
• Atom Count: 3,680 
• Modeled Residue Count: 430 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain	A [auth AAA], B [auth BBB]	232	Homo sapiens	Mutation(s): 2
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-(1-2)-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 [auth AaA], D [auth BaB]	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G33244HE GlyCosmos: G33244HE GlyGen: G33244HE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	E [auth AAA]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.302 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.244 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.023	α = 90
b = 79.74	β = 90
c = 142.478	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Shenoy, A., Barb, A.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U01 AI148114

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release