4NEM | pdb_00004nem

Small molecular fragment bound to crystal contact interface of Interleukin-2

• PDB DOI: https://doi.org/10.2210/pdb4NEM/pdb

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


• Deposited: 2013-10-29 Released: 2014-11-19 
• Deposition Author(s): Jehle, S., Brenke, R., Vajda, S., Allen, K.N., Kozakov, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Small molecular fragments bound to binding energy hot-spot in crystal contact interface of Interleukin-2

Jehle, S., Brenke, R., Vajda, S., Allen, K.N., Kozakov, D.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 15.44 kDa 
• Atom Count: 968 
• Modeled Residue Count: 114 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2	A	130	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens) Explore P60568  Go to UniProtKB:  P60568
PHAROS:  P60568 GTEx:  ENSG00000109471

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2JY	B [auth A]	5-[(2,3-dichlorophenoxy)methyl]furan-2-carboxylic acid C12 H8 Cl2 O4 DGUXQMFHNWGUES-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.709	α = 90
b = 48.544	β = 90
c = 79.767	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Jehle, S., Brenke, R., Vajda, S., Allen, K.N., Kozakov, D.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary