9MIU | pdb_00009miu

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-9-039SRM.

• PDB DOI: https://doi.org/10.2210/pdb9MIU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-13 Released: 2024-12-25 
• Deposition Author(s): Minasov, G., Winsor, J., Roy, S.M., Watterson, D.M., Shuvalova, L.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.197 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-9-039SRM.

Minasov, G., Winsor, J., Roy, S.M., Watterson, D.M., Shuvalova, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.61 kDa 
• Atom Count: 2,559 
• Modeled Residue Count: 276 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	304	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
A1BLJ (Subject of Investigation/LOI)	B [auth A]	6-chloro-N,N-dimethyl-5-(pyridin-4-yl)pyridazin-3-amine C11 H11 Cl N4 TXDDCILZWXYXEH-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.197 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.986	α = 90
b = 62.627	β = 90
c = 88.501	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Minasov, G., Winsor, J., Roy, S.M., Watterson, D.M., Shuvalova, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG066722

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release