9N2M | pdb_00009n2m

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM

• PDB DOI: https://doi.org/10.2210/pdb9N2M/pdb

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


• Deposited: 2025-01-29 Released: 2025-04-02 
• Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.177 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM

Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 34.08 kDa 
• Atom Count: 2,606 
• Modeled Residue Count: 280 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	293	Homo sapiens	Mutation(s): 0  Gene Names: DAPK1, DAPK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53355 (Homo sapiens) Explore P53355  Go to UniProtKB:  P53355
PHAROS:  P53355 GTEx:  ENSG00000196730

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BVM	C [auth A]	5-(pyridin-4-yl)-3-[4-(pyridin-4-yl)piperazin-1-yl]pyridazine C18 H18 N6 PMYQZDHMSFEWMS-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.177 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.3	α = 90
b = 63.08	β = 90
c = 88.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release