3GU5

Crystal structure of DAPKQ23V-AMPPNP-Mg2+

• PDB DOI: https://doi.org/10.2210/pdb3GU5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-03-28 Released: 2010-03-09 
• Deposition Author(s): McNamara, L.K., Schavocky, J.S., Watterson, D.M., Brunzelle, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.219 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Enzyme activity and crystallographic analyses of a glycine-rich loop mutant of DAPK

McNamara, L.K., Schavocky, J.S., Watterson, D.M., Brunzelle, J.S.

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: 34.43 kDa 
• Atom Count: 2,753 
• Modelled Residue Count: 280 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	295	Homo sapiens	Mutation(s): 1  Gene Names: DAPK, DAPK1, death-associated protein kinase 1 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
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.219 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.919	α = 90
b = 62.47	β = 90
c = 88.555	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): McNamara, L.K., Schavocky, J.S., Watterson, D.M., Brunzelle, J.S.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description