4YQX

Mouse IL-2 Bound to JES6-1 scFv Fragment

• PDB DOI: https://doi.org/10.2210/pdb4YQX/pdb

• Classification: CYTOKINE/IMMUNE SYSTEM
• Organism(s): Rattus norvegicus, Mus musculus
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-13 Released: 2015-07-01 
• Deposition Author(s): Spangler, J.B., Luca, V.C., Jude, K.M., Garcia, K.C.
• 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: 2.83 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.95 kDa 
• Atom Count: 5,824 
• Modelled Residue Count: 719 
• Deposited Residue Count: 742 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JES6-1 VH domain	A [auth H], D [auth N]	123	Rattus norvegicus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
JES6-1 VL domain	B [auth L], E [auth O]	118	Rattus norvegicus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2	C [auth A], F [auth M]	130	Mus musculus	Mutation(s): 0  Gene Names: Il2, Il-2
UniProt
Find proteins for P04351 (Mus musculus) Explore P04351  Go to UniProtKB:  P04351

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth B]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G63564LA GlyCosmos:  G63564LA

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.024	α = 90
b = 99.024	β = 90
c = 198.7	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Spangler, J.B., Luca, V.C., Jude, K.M., Garcia, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI108626

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-07-08
  Changes: Source and taxonomy
• Version 1.2: 2017-07-26
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary