Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.73 kDa 
• Atom Count: 972 
• Modelled Residue Count: 114 
• Deposited 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

• PDB DOI: 10.2210/pdb1M4A/pdb

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


• 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 
• R-Value Observed: 0.276 

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 U S A 100: 1603-1608

• PubMed: 12582206 
• DOI: 10.1073/pnas.252756299
• Primary Citation of Related Structures:  
  1M47, 1M48, 1M49, 1M4A, 1M4B, 1M4C


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
interleukin-2	A	133	Homo sapiens	Mutation(s): 1  Gene Names: IL2
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens) Explore P60568  Go to UniProtKB:  P60568
PHAROS:  P60568

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPE	B [auth A]	(1H-INDOL-3-YL)-(2-MERCAPTO-ETHOXYIMINO)-ACETIC ACID C12 H14 N2 O3 S FJAWIBGKKKXXAL-LLVKDONJSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.324 
• R-Value Work: 0.271 
• R-Value Observed: 0.276 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.15	α = 90
b = 47.59	β = 104.84
c = 42.63	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations