Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.18 kDa 
• Atom Count: 3691 
• Modelled Residue Count: 450 
• Deposited Residue Count: 452 
• Unique protein chains: 1

1KSW

Structure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Complex with N6-benzyl ADP

• PDB DOI: 10.2210/pdb1KSW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2002-01-14 Released: 2002-02-27 
• Deposition Author(s): Witucki, L.A., Huang, X., Shah, K., Liu, Y., Kyin, S., Eck, M.J., Shokat, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.294 
• R-Value Work: 0.231 

Literature

Mutant tyrosine kinases with unnatural nucleotide specificity retain the structure and phospho-acceptor specificity of the wild-type enzyme.

Witucki, L.A., Huang, X., Shah, K., Liu, Y., Kyin, S., Eck, M.J., Shokat, K.M.

(2002) Chem Biol 9: 25-33

• PubMed: 11841936 
• DOI: 10.1016/s1074-5521(02)00091-1
• Primary Citation of Related Structures:  
  1KSW


• PubMed Abstract: 
  

The direct substrates of one protein kinase in a cell can be identified by mutation of the ATP binding pocket to allow an unnatural ATP analog to be accepted exclusively by the engineered kinase. Here, we present structural and functional assessment of peptide specificity of mutant protein kinases with unnatural ATP analogs. The crystal structure (2.8 A resolution) of c-Src (T338G) with N(6)-(benzyl) ADP bound shows that the creation of a unique nucleotide binding pocket does not alter the phospho-acceptor binding site of the kinase. A panel of optimal peptide substrates of defined sequence, as well as a degenerate peptide library, was utilized to assess the phospho-acceptor specificity of the engineered "traceable" kinases. The specificity profiles for the mutant kinases were found to be identical to those of their wild-type counterparts.

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Organizational Affiliation: 

Department of Cellular and Molecular Pharmacology, Box 0450, University of California, San Francisco 94143-0450, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC	A	452	Homo sapiens	Mutation(s): 2  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 GTEx:  ENSG00000197122

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NBS	B [auth A]	N6-BENZYL ADENOSINE-5'-DIPHOSPHATE C17 H21 N5 O10 P2 MRHGMAGSDAQUFH-LSCFUAHRSA-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:  1KSW	-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: 2.80 Å
• R-Value Free: 0.294 
• R-Value Work: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.81	α = 90
b = 87.68	β = 90
c = 106.28	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-14 
• Released Date: 2002-02-27 
Deposition Author(s): Witucki, L.A., Huang, X., Shah, K., Liu, Y., Kyin, S., Eck, M.J., Shokat, K.M.

Revision History  

• Version 1.0: 2002-02-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations