5VME

Crystal structure of human IgG1 Fc K248E, T437R mutant

• PDB DOI: https://doi.org/10.2210/pdb5VME/pdb

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


• Deposited: 2017-04-27 Released: 2017-08-30 
• Deposition Author(s): Armstrong, A.A., Gilliland, G.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

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: gel filtration

Macromolecule Content

• Total Structure Weight: 53.09 kDa 
• Atom Count: 3,206 
• Modelled Residue Count: 403 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human IgG1 Fc K248E,T437R mutant	A, B	223	Homo sapiens	Mutation(s): 2  Gene Names: DKFZp686C11235
UniProt
Find proteins for Q6MZV7 (Homo sapiens) Explore Q6MZV7  Go to UniProtKB:  Q6MZV7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	C	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80858MF GlyCosmos:  G80858MF GlyGen:  G80858MF

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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: 3.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.01	α = 90
b = 115.01	β = 90
c = 73.58	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Armstrong, A.A., Gilliland, G.L.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Database references
• Version 1.2: 2017-10-11
  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: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary