Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.72 kDa 
• Atom Count: 1770 
• Residue Count: 217 
• Unique protein chains: 2

1A1B

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

• DOI: 10.2210/pdb1A1B/pdb

• Classification: COMPLEX (TRANSFERASE/PEPTIDE)
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1997-12-10 Released: 1998-04-08 
• Deposition Author(s): Shewchuk, L., Jordan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

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

• PubMed: 9174343 
• DOI: 10.1021/bi970019n
• Primary Citation of Related Structures:  
  1A07, 1A09, 1A08, 1A1E, 1A1C, 1A1B, 1A1A


• 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. 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.

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Organizational Affiliation: 

Department of Structural Chemistry, Glaxo Wellcome, Inc., Research Triangle Park, North Carolina 27709, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-SRC TYROSINE KINASE	A, B	107	Homo sapiens	Mutation(s): 0  Gene Names: SRC, SRC1 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P12931 (Homo sapiens) Explore P12931  Go to UniProtKB:  P12931
NIH Common Fund Data Resources
PHAROS:  P12931 GTEx:  ENSG00000197122

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)	C, D	4	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	C,D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.5	α = 90
b = 67.1	β = 90
c = 74.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
bioteX	data reduction
bioteX	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-12-10 
• Released Date: 1998-04-08 
Deposition Author(s): Shewchuk, L., Jordan, S.

Revision History 

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