1FMK

CRYSTAL STRUCTURE OF HUMAN TYROSINE-PROTEIN KINASE C-SRC

• PDB DOI: https://doi.org/10.2210/pdb1FMK/pdb

• Classification: PHOSPHOTRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


• Deposited: 1997-01-24 Released: 1997-08-20 
• Deposition Author(s): Xu, W., Harrison, S.C., Eck, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.264 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Three-dimensional structure of the tyrosine kinase c-Src.

Xu, W., Harrison, S.C., Eck, M.J.

(1997) Nature 385: 595-602

• PubMed: 9024657 
• DOI: https://doi.org/10.1038/385595a0
• Primary Citation of Related Structures:  
  1FMK


• PubMed Abstract: 
  

  The structure of a large fragment of the c-Src tyrosine kinase, comprising the regulatory and kinase domains and the carboxy-terminal tall, has been determined at 1.7 A resolution in a closed, inactive state. Interactions among domains, stabilized by binding of the phosphorylated tail to the SH2 domain, lock the molecule in a conformation that simultaneously disrupts the kinase active site and sequesters the binding surfaces of the SH2 and SH3 domains. The structure shows how appropriate cellular signals, or transforming mutations in v-Src, could break these interactions to produce an open, active kinase.

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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: 51.71 kDa 
• Atom Count: 4,006 
• Modelled Residue Count: 438 
• 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

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:  1FMK	-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: 0.264 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.759	α = 90
b = 87.38	β = 90
c = 101.295	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: 1997-08-20 
Deposition Author(s): Xu, W., Harrison, S.C., Eck, M.J.

Revision History  

• Version 1.0: 1997-08-20
  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: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-09
  Changes: Structure summary