6KA7 | pdb_00006ka7

The complex structure of Human IgG Fc and its binding Repebody

• PDB DOI: https://doi.org/10.2210/pdb6KA7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-21 Released: 2020-06-24 
• Deposition Author(s): Choi, J., Kim, H.
• Funding Organization(s): Ministry of Education (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.333 (Depositor), 0.331 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Literature

The complex structure of Human IgG Fc and its binding Repebody

Choi, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 107.4 kDa 
• Atom Count: 6,718 
• Modeled Residue Count: 860 
• Deposited Residue Count: 928 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
repebody	A, B	256	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain	C, D	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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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	E, F	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G80858MF GlyCosmos: G80858MF GlyGen: G80858MF

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.333 (Depositor), 0.331 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.926	α = 90
b = 107.42	β = 90
c = 171.35	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Choi, J., Kim, H.

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Funding Organization	Location	Grant Number
Ministry of Education (Korea)	Korea, Republic Of	2017R1A6A3A04012313

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary