3OV1

Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Protein-ligand interactions: thermodynamic effects associated with increasing nonpolar surface area.

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

(2011) J Am Chem Soc 133: 18518-18521

  • DOI: 10.1021/ja2068752
  • Primary Citation of Related Structures:  
    3OV1, 3OVE, 3S8L, 3S8N, 3S8O

  • PubMed Abstract: 

    • Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and Ac-pTyr-Xaa-Asn derived tripeptides in which the Xaa residue is an α,α-cycloaliphatic amino acid that varies in ring size from three- to seven-membered. Althou ...

    Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and Ac-pTyr-Xaa-Asn derived tripeptides in which the Xaa residue is an α,α-cycloaliphatic amino acid that varies in ring size from three- to seven-membered. Although the six- and seven-membered ring analogs are approximately equipotent, binding affinities of those having three- to six-membered rings increase incrementally with ring size because increasingly more favorable binding enthalpies dominate increasingly less favorable binding entropies, a finding consistent with an enthalpy-driven hydrophobic effect. Crystallographic analysis reveals that the only significant differences in structures of the complexes are in the number of van der Waals contacts between the domain and the methylene groups in the Xaa residues. There is a positive correlation between buried nonpolar surface area and binding free energy and enthalpy, but not with ΔC(p). Displacing a water molecule from a protein-ligand interface is not necessarily reflected in a favorable change in binding entropy. These findings highlight some of the fallibilities associated with commonly held views of relationships of structure and energetics in protein-ligand interactions and have significant implications for ligand design.

    Organizational Affiliation: 

    Chemistry and Biochemistry Department, Institute of Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Growth factor receptor-bound protein 2 A117Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PYAC3CN B5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
FMT
Query on FMT
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A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
1AC
Query on 1AC		BPEPTIDE LINKINGC4 H7 N O2ALA
PTR
Query on PTR		BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.131α = 90
b = 42.131β = 90
c = 108.983γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references