2SRC

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

• PDB DOI: https://doi.org/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 

Starting Model: experimental

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: https://doi.org/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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.22 kDa 
• Atom Count: 3,915 
• Modelled Residue Count: 450 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN KINASE SRC	A	452	Homo sapiens	Mutation(s): 1  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 GTEx:  ENSG00000197122

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
PTR	BindingDB:  2SRC	-TΔS: -1.81e+1 (kJ/mol) from 1 assay(s)
		ΔG: -2.14e+1 (kJ/mol) from 1 assay(s)

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

• 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
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary