3DK7 | pdb_00003dk7

Crystal structure of mutant ABL kinase domain in complex with small molecule fragment

• PDB DOI: https://doi.org/10.2210/pdb3DK7/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-06-24 Released: 2008-07-29 
• Deposition Author(s): Lewis, H.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 

Literature

Crystal structure of mutant ABL kinase domain in complex with small molecule fragment

Bounaud, P.-Y., Gosberg, A., Hendle, J., Lewis, H.A., Romero, R., Wilson, M.E., Zhang, F.

To be published.

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: 64.97 kDa 
• Atom Count: 4,563 
• Modeled Residue Count: 535 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase ABL1	A, B	277	Mus musculus	Mutation(s): 2  Gene Names: Abl1, Abl EC: 2.7.10.2
UniProt
Find proteins for P00520 (Mus musculus) Explore P00520  Go to UniProtKB:  P00520

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SX7	C [auth A], F [auth B]	2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide C21 H22 N6 O INAGORZAOFUKOZ-UHFFFAOYSA-N
SO4	D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.941	α = 90
b = 132.712	β = 90
c = 56.297	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Lewis, H.A.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-11-20
  Changes: Data collection, Structure summary