Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 62594.47 
• Atom Count: 4087 
• Residue Count: 512 
• Unique protein chains: 3

6DG5

Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic complex with IL-2Rb and IL-2Rg

• DOI: 10.2210/pdb6DG5/pdb

• Classification: BIOSYNTHETIC PROTEIN/Protein Binding
• Organism(s): Mus musculus
• Expression System: Escherichia coli, Trichoplusia ni


• Deposited: 2018-05-16 Released: 2019-01-16 
• Deposition Author(s): Jude, K.M., Silva, D.-A., Yu, S., Baker, D., Garcia, K.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.516 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 

Literature

De novo design of potent and selective mimics of IL-2 and IL-15.

Silva, D.A., Yu, S., Ulge, U.Y., Spangler, J.B., Jude, K.M., Labao-Almeida, C., Ali, L.R., Quijano-Rubio, A., Ruterbusch, M., Leung, I., Biary, T., Crowley, S.J., Marcos, E., Walkey, C.D., Weitzner, B.D., Pardo-Avila, F., Castellanos, J., Carter, L., Stewart, L., Riddell, S.R., Pepper, M., Bernardes, G.J.L., Dougan, M., Garcia, K.C., Baker, D.

(2019) Nature 565: 186-191

• PubMed: 30626941 
• Primary Citation of Related Structures:  
  6DG6

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Neoleukin-2/15	A	104	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-2 receptor subunit beta	B	209	Mus musculus	Mutation(s): 0  Gene Names: Il2rb
Find proteins for P16297 (Mus musculus) Go to UniProtKB:  P16297

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Cytokine receptor common subunit gamma	C	199	Mus musculus	Mutation(s): 0  Gene Names: Il2rg
Find proteins for P34902 (Mus musculus) Go to UniProtKB:  P34902

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	B	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	B	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
BMA	B	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	B, C	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.516 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2 2₁
• Diffraction Data DOI: 
  10.15785/SBGRID/588 SBGrid

Unit Cell:

Length (Å)	Angle (°)
a = 65.125	α = 90.00
b = 67.914	β = 90.00
c = 172.084	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction
BUSTER	refinement
Aimless	data scaling
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-16 
• Released Date: 2019-01-16 
• Deposition Author(s): Jude, K.M., Silva, D.-A., Yu, S., Baker, D., Garcia, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	RO1-AI51321

Revision History 

• Version 1.0: 2019-01-16
  Type: Initial release
• Version 1.1: 2019-01-23
  Type: Data collection, Database references