6IN4

Crystal structure of apo DAPK1 in the presence of 18-crown-6

• PDB DOI: https://doi.org/10.2210/pdb6IN4/pdb

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


• Deposited: 2018-10-24 Released: 2019-10-30 
• Deposition Author(s): Yokoyama, T., Kosaka, Y., Matsumoto, K., Kitakami, R., Nabeshima, Y., Mizuguchi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Literature

Crown Ethers as Transthyretin Amyloidogenesis Inhibitor

Yokoyama, T., Kosaka, Y., Matsumoto, K., Kitakami, R., Nabeshima, Y., Mizuguchi, M.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.89 kDa 
• Atom Count: 2,386 
• Modelled Residue Count: 265 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.675	α = 90
b = 62.36	β = 90
c = 88.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Yokoyama, T., Kosaka, Y., Matsumoto, K., Kitakami, R., Nabeshima, Y., Mizuguchi, M.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references