3DO3 | pdb_00003do3

Human 1gG1 Fc fragment, 2.5 Angstrom structure

• PDB DOI: https://doi.org/10.2210/pdb3DO3/pdb

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


• Deposited: 2008-07-03 Released: 2009-07-21 
• Deposition Author(s): Braden, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.330 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.280 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.280 (Depositor) 

Starting Model: experimental

Literature

Human 1gG1 Fc fragment, 2.5 Angstrom structure.

Braden, B.C.

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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.27 kDa 
• Atom Count: 3,664 
• Modeled Residue Count: 419 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B	212	Homo sapiens	Mutation(s): 2  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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01857-2

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, D	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G33244HE GlyCosmos: G33244HE GlyGen: G33244HE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.330 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.280 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.280 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.2053	α = 90
b = 80.2157	β = 90
c = 138.7493	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Braden, B.C.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary