Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 14.45 kDa 
• Atom Count: 923 
• Residue Count: 105 
• Unique protein chains: 2

4P9V

Grb2 SH2 complexed with a pTyr-Ac6cN-Asn tripeptide

• DOI: 10.2210/pdb4P9V/pdb

• Classification: Signaling Protein/Antagonist
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-06 Released: 2014-06-18 
• Deposition Author(s): Clements, J.H., Martin, S.F.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Robert A. Welch Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.257 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Protein-ligand interactions: Probing the energetics of a putative cation-pi interaction.

Myslinski, J.M., Clements, J.H., Martin, S.F.

(2014) Bioorg Med Chem Lett 24: 3164-3167

• PubMed: 24856058 
• DOI: 10.1016/j.bmcl.2014.04.114
• Primary Citation of Related Structures:  
  4P9V, 4P9Z


• PubMed Abstract: 
  

In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO-pTyr-Ac6c-Asn wherein the R group is varied to include different alkyl, cycloalkyl, and aryl groups. Although an indole ring is reputed to have the strongest interaction with a guanidinium ion, binding free energies, ΔG°, for derivatives of RCO-pTyr-Ac6c-Asn bearing cyclohexyl and phenyl groups were slightly more favorable than their indolyl analog. Crystallographic analysis of two complexes reveals that test ligands bind in similar poses with the notable exception of the relative orientation and proximity of the phenyl and indolyl rings relative to an arginine residue of the domain. These spatial orientations are consistent with those observed in other cation-π interactions, but there is no net energetic benefit to such an interaction in this biological system. Accordingly, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.

---

Organizational Affiliation: 

The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 2	A	117	Homo sapiens	Mutation(s): 0  Gene Names: GRB2, ASH
Find proteins for P62993 (Homo sapiens) Explore P62993  Go to UniProtKB:  P62993
NIH Common Fund Data Resources
PHAROS:  P62993 GTEx:  ENSG00000177885

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHQ-PTR-02K-ASN-NH2	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
02K	B	PEPTIDE LINKING	C7 H13 N O2		ALA
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.257 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.935	α = 90
b = 41.935	β = 90
c = 108.715	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-04-06 
• Released Date: 2014-06-18 
Deposition Author(s): Clements, J.H., Martin, S.F.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM 84965
National Science Foundation (NSF, United States)	United States	CHE 0750329
Robert A. Welch Foundation	United States	F-652

Revision History 

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2014-07-16
  Changes: Database references
• Version 1.2: 2014-12-24
  Changes: Database references
• Version 1.3: 2017-08-09
  Changes: Database references, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2017-09-27
  Changes: Author supporting evidence
• Version 1.5: 2019-11-27
  Changes: Author supporting evidence