3BQR

Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with an imidazo-pyridazine ligand

• PDB DOI: https://doi.org/10.2210/pdb3BQR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-20 Released: 2008-02-26 
• Deposition Author(s): Filippakopoulos, P., Rellos, P., Fedorov, O., Niesen, F., Pike, A.C.W., Pilka, E.S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Crystal Structure of Human Death Associated Protein Kinase 3 (DAPK3) in Complex with an Imidazo-Pyridazine Ligand.

Filippakopoulos, P., Rellos, P., Fedorov, O., Niesen, F., Pike, A.C.W., Pilka, E.S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.12 kDa 
• Atom Count: 2,571 
• Modelled Residue Count: 275 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 3	A	283	Homo sapiens	Mutation(s): 0  Gene Names: DAPK3, ZIPK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43293 (Homo sapiens) Explore O43293  Go to UniProtKB:  O43293
GTEx:  ENSG00000167657

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4RB	B [auth A]	4-(6-{[(1R)-1-(hydroxymethyl)propyl]amino}imidazo[1,2-b]pyridazin-3-yl)benzoic acid C17 H18 N4 O3 KKZYGUVAFJCULH-CYBMUJFWSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGO	C [auth A], D [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.533	α = 90
b = 83.533	β = 90
c = 113.693	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Filippakopoulos, P., Rellos, P., Fedorov, O., Niesen, F., Pike, A.C.W., Pilka, E.S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description