1A07

C-SRC (SH2 DOMAIN) COMPLEXED WITH ACE-MALONYL TYR-GLU-(N,N-DIPENTYL AMINE)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Peptide ligands of pp60(c-src) SH2 domains: a thermodynamic and structural study.

Charifson, P.S., Shewchuk, L.M., Rocque, W., Hummel, C.W., Jordan, S.R., Mohr, C., Pacofsky, G.J., Peel, M.R., Rodriguez, M., Sternbach, D.D., Consler, T.G.

(1997) Biochemistry 36: 6283-6293

  • DOI: 10.1021/bi970019n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Thermodynamic measurements, structural determinations, and molecular computations were applied to a series of peptide ligands of the pp60(c-src) SH2 domain in an attempt to understand the critical binding determinants for this class of molecules. Iso ...

    Thermodynamic measurements, structural determinations, and molecular computations were applied to a series of peptide ligands of the pp60(c-src) SH2 domain in an attempt to understand the critical binding determinants for this class of molecules. Isothermal titration calorimetry (ITC) measurements were combined with structural data derived from X-ray crystallographic studies on 12 peptide-SH2 domain complexes. The peptide ligands studied fall into two general classes: (1) dipeptides of the general framework N-acetylphosphotyrosine (or phosphotyrosine replacement)-Glu or methionine (or S-methylcysteine)-X, where X represents a hydrophobic amine, and (2) tetra- or pentapeptides of the general framework N-acetylphosphotyrosine-Glu-Glu-Ile-X, where X represents either Glu, Gln, or NH2. Dipeptide analogs which featured X as either hexanolamine or heptanolamine were able to pick up new hydrogen bonds involving their hydroxyl groups within a predominantly lipophilic surface cavity. However, due to internal strain as well as the solvent accessibility of the new hydrogen bonds formed, no net increase in binding affinity was observed. Phosphatase-resistant benzylmalonate and alpha,alpha-difluorobenzyl phosphonate analogs of phosphotyrosine retained some binding affinity for the pp60(c-src) SH2 domain but caused local structural perturbations in the phosphotyrosine-binding site. In the case where a reversible covalent thiohemiacetal was formed between a formylated phosphotyrosine analog and the thiol side chain of Cys-188, deltaS was 25.6 cal/(mol K) lower than for the nonformylated phosphotyrosine parent. Normal mode calculations show that the dramatic decrease in entropy observed for the covalent thiohemiacetal complex is due to the inability of the phosphotyrosine moiety to transform lost rotational and translational degrees of freedom into new vibrational modes.

    Organizational Affiliation: 

    Department of Structural Chemistry, Glaxo Wellcome, Inc., Research Triangle Park, North Carolina 27709, USA. psc11602@glaxo.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-SRC TYROSINE KINASE
A, B
107Homo sapiensMutation(s): 0 
Gene Names: SRC (SRC1)
EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens)
Go to Gene View: SRC
Go to UniProtKB:  P12931
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACE-MALONYL TYR-GLU-(N,N-DIPENTYL AMINE)
C, D
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
DIP
Query on DIP
C, D
NON-POLYMERC10 H23 N

--

PTR
Query on PTR
C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PTRΔG: -21.4 kJ/mol (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.500α = 90.00
b = 67.200β = 90.00
c = 74.500γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata scaling
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
R-AXISdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection, Other