3DFC | pdb_00003dfc

Crystal structure of a glycine-rich loop mutant of the death associated protein kinase catalytic domain with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb3DFC/pdb

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


• Deposited: 2008-06-11 Released: 2009-05-26 
• Deposition Author(s): McNamara, L.K., Schavocky, J.P., Watterson, D.M., Brunzelle, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

High resolution crystal structures of the death associated protein kinase catalytic domain with a key point mutation in the glycine-rich loop

McNamara, L.K., Schavocky, J.P., 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: 2,584 
• Modeled 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 [auth B]	295	Homo sapiens	Mutation(s): 1  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
ANP	B	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.688	α = 90
b = 62.444	β = 90
c = 88.602	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): McNamara, L.K., Schavocky, J.P., Watterson, D.M., Brunzelle, J.S.

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-01-27
  Changes: Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description