1A07

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

PDB DOI: 10.2210/pdb1A07/pdb

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

Deposited: 1997-12-09 Released: 1998-04-08
Deposition Author(s): Shewchuk, L., Jordan, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work: 0.192
R-Value Observed: 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

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

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.

Organizational Affiliation:

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-SRC TYROSINE KINASE	A, C [auth B]	107	Homo sapiens	Mutation(s): 0 Gene Names: SRC, SRC1 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens) Explore P12931 Go to UniProtKB: P12931
PHAROS: P12931
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12931
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-MALONYL TYR-GLU-(N,N-DIPENTYL AMINE)	B [auth C], D	4	N/A	Mutation(s): 0
Protein Feature View Expand
Reference Sequence