4YPD | pdb_00004ypd

Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine

• PDB DOI: https://doi.org/10.2210/pdb4YPD/pdb

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


• Deposited: 2015-03-12 Released: 2015-05-13 
• Deposition Author(s): Grum-Tokars, V.L., Minasov, G., Roy, S.M., Anderson, W.F., Watterson, D.M.
• 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: 1.40 Å
• R-Value Free: 
  0.177 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of DAPK1 catalytic domain in complex with hinge binding fragments

Grum-Tokars, V.L., Minasov, G., Roy, S.M., Anderson, W.F., 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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.02 kDa 
• Atom Count: 2,909 
• Modeled Residue Count: 281 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	294	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DKG	D [auth A]	4-methylpyridazine C5 H6 N2 AIKUBOPKWKZULG-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.177 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.853	α = 90
b = 62.511	β = 90
c = 88.193	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Grum-Tokars, V.L., Minasov, G., Roy, S.M., Anderson, W.F., Watterson, D.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	U01AG043415

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description