Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15734.36 
• Atom Count: 959 
• Residue Count: 133 
• Unique protein chains: 1

1M4A

Crystal Structure of Human Interleukin-2 Y31C Covalently Modified at C31 with (1H-Indol-3-yl)-(2-mercapto-ethoxyimino)-acetic acid

• DOI: 10.2210/pdb1M4A/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): 1 


• Deposited: 2002-07-02 Released: 2002-07-31 
• Deposition Author(s): Arkin, M.A., Randal, M., DeLano, W.L., Hyde, J., Luong, T.N., Oslob, J.D., Raphael, D.R., Taylor, L., Wang, J., McDowell, R.S., Wells, J.A., Braisted, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.324 
• R-Value Work: 0.271 

Literature

Binding of small molecules to an adaptive protein-protein interface

Arkin, M.A., Randal, M., DeLano, W.L., Hyde, J., Luong, T.N., Oslob, J.D., Raphael, D.R., Taylor, L., Wang, J., McDowell, R.S., Wells, J.A., Braisted, A.C.

(2003) Proc.Natl.Acad.Sci.USA 100: 1603-1608

• PubMed: 12582206 
• DOI: 10.1073/pnas.252756299
• Primary Citation of Related Structures:  
  1M4C, 1M4B, 1M49, 1M48, 1M47


• PubMed Abstract: 
  

Understanding binding properties at protein-protein interfaces has been limited to structural and mutational analyses of natural binding partners or small peptides identified by phage display. Here, we present a high-resolution analysis of a nonpeptidyl small molecule, previously discovered by medicinal chemistry [Tilley, J. W., et al. (1997) J. Am. Chem. Soc. 119, 7589-7590], which binds to the cytokine IL-2. The small molecule binds to the same site that binds the IL-2 alpha receptor and buries into a groove not seen in the free structure of IL-2. Comparison of the bound and several free structures shows this site to be composed of two subsites: one is rigid, and the other is highly adaptive. Thermodynamic data suggest the energy barriers between these conformations are low. The subsites were dissected by using a site-directed screening method called tethering, in which small fragments were captured by disulfide interchange with cysteines introduced into IL-2 around these subsites. X-ray structures with the tethered fragments show that the subsite-binding interactions are similar to those observed with the original small molecule. Moreover, the adaptive subsite tethered many more compounds than did the rigid one. Thus, the adaptive nature of a protein-protein interface provides sites for small molecules to bind and underscores the challenge of applying structure-based design strategies that cannot accurately predict a dynamic protein surface.

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Organizational Affiliation: 

Department of Biology, Sunesis Pharmaceuticals, South San Francisco, CA 94080-1913, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
interleukin-2	A	133	Homo sapiens	Mutation(s): 1  Gene Names: IL2
Find proteins for P60568 (Homo sapiens) Go to Gene View: IL2 Go to UniProtKB:  P60568

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MPE	A	(1H-INDOL-3-YL)-(2-MERCAPTO-ETHOXYIMINO)-ACETIC ACID C12 H14 N2 O3 S FJAWIBGKKKXXAL-LLVKDONJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.324 
• R-Value Work: 0.271 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 31.150	α = 90.00
b = 47.590	β = 104.84
c = 42.630	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling
AMoRE	phasing
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-02 
• Released Date: 2002-07-31 
• Deposition Author(s): Arkin, M.A., Randal, M., DeLano, W.L., Hyde, J., Luong, T.N., Oslob, J.D., Raphael, D.R., Taylor, L., Wang, J., McDowell, R.S., Wells, J.A., Braisted, A.C.

Revision History 

• Version 1.0: 2002-07-31
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description