Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.22 kDa 
• Atom Count: 3915 
• Modelled Residue Count: 450 
• Deposited Residue Count: 452 
• Unique protein chains: 1

2SRC

CRYSTAL STRUCTURE OF HUMAN TYROSINE-PROTEIN KINASE C-SRC, IN COMPLEX WITH AMP-PNP

• DOI: 10.2210/pdb2SRC/pdb

• Classification: TYROSINE-PROTEIN KINASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 1998-12-29 Released: 1999-07-22 
• Deposition Author(s): Xu, W., Doshi, A., Lei, M., Eck, M.J., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Crystal structures of c-Src reveal features of its autoinhibitory mechanism.

Xu, W., Doshi, A., Lei, M., Eck, M.J., Harrison, S.C.

(1999) Mol Cell 3: 629-638

• PubMed: 10360179 
• DOI: 10.1016/s1097-2765(00)80356-1
• Primary Citation of Related Structures:  
  2SRC


• PubMed Abstract: 
  

Src family kinases are maintained in an assembled, inactive conformation by intramolecular interactions of their SH2 and SH3 domains. Full catalytic activity requires release of these restraints as well as phosphorylation of Tyr-416 in the activation loop. In previous structures of inactive Src kinases, Tyr-416 and flanking residues are disordered. We report here four additional c-Src structures in which this segment adopts an ordered but inhibitory conformation. The ordered activation loop forms an alpha helix that stabilizes the inactive conformation of the kinase domain, blocks the peptide substrate-binding site, and prevents Tyr-416 phosphorylation. Disassembly of the regulatory domains, induced by SH2 or SH3 ligands, or by dephosphorylation of Tyr-527, could lead to exposure and phosphorylation of Tyr-416.

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Organizational Affiliation: 

Laboratory of Molecular Medicine, Children's Hospital, Boston, Massachusetts 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN KINASE SRC	A	452	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	A	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PTR	-TΔS:  18.100000381469727   kJ/mol  BindingDB
PTR	ΔG:  21.399999618530273   kJ/mol  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.59	α = 90
b = 72.97	β = 90
c = 172.69	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-12-29 
• Released Date: 1999-07-22 
Deposition Author(s): Xu, W., Doshi, A., Lei, M., Eck, M.J., Harrison, S.C.

Revision History  

• Version 1.0: 1999-07-22
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance