5SWH | pdb_00005swh

c-Src V281C kinase domain in complex with Rao-IV-151

• PDB DOI: https://doi.org/10.2210/pdb5SWH/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-08-08 Released: 2017-08-16 
• Deposition Author(s): Merritt, E.A., Dieter, E.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

A combined approach reveals a regulatory mechanism coupling Src's kinase activity, localization, and phosphotransferase-independent functions

Register, A.C., Maly, D.J.

(2019) Mol Cell 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.34 kDa 
• Atom Count: 4,243 
• Modeled Residue Count: 519 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 1  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
71D	C [auth A], D [auth B]	(2R)-3-[4-amino-5-(4-chlorophenyl)-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)propanami de C22 H25 Cl N6 O2 GWOKLTYKEJQNOY-OAHLLOKOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.819	α = 77.94
b = 64.139	β = 89.5
c = 74.91	γ = 89.83

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Merritt, E.A., Dieter, E.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM086858

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2024-11-13
  Changes: Structure summary