5LGJ

THE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C

• PDB DOI: https://doi.org/10.2210/pdb5LGJ/pdb

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


• Deposited: 2016-07-07 Released: 2017-03-15 
• Deposition Author(s): Dhaliwal, B., Pang, M.O.Y., Sutton, B.J.
• Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust, Asthma UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.248 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

THE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C

Dhaliwal, B., Pang, M.O.Y., Keeble, A.H., Taylor, A.I., James, L.K., Gould, H.J., McDonnell, J.M., Beavil, A.J., Sutton, B.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.13 kDa 
• Atom Count: 5,305 
• Modelled Residue Count: 624 
• Deposited Residue Count: 639 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig epsilon chain C region	A	319	Homo sapiens	Mutation(s): 1  Gene Names: IGHE
UniProt & NIH Common Fund Data Resources
Find proteins for P01854 (Homo sapiens) Explore P01854  Go to UniProtKB:  P01854
PHAROS:  P01854 GTEx:  ENSG00000211891

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig epsilon chain C region	B	320	Homo sapiens	Mutation(s): 1  Gene Names: IGHE
UniProt & NIH Common Fund Data Resources
Find proteins for P01854 (Homo sapiens) Explore P01854  Go to UniProtKB:  P01854
PHAROS:  P01854 GTEx:  ENSG00000211891

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G10756ZZ GlyCosmos:  G10756ZZ GlyGen:  G10756ZZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G76464YC GlyCosmos:  G76464YC GlyGen:  G76464YC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	H [auth A], I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.248 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.45	α = 90
b = 74.91	β = 90
c = 79.06	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data collection
Aimless	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Dhaliwal, B., Pang, M.O.Y., Sutton, B.J.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--
Wellcome Trust	United Kingdom	--
Asthma UK	United Kingdom	--

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2018-10-24
  Changes: Advisory, Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary