2Y4P | pdb_00002y4p

Dimeric structure of DAPK-1 catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb2Y4P/pdb

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


• Deposited: 2011-01-07 Released: 2012-01-18 
• Deposition Author(s): de Diego, I., Lehmann, F., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.312 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

A Journey Through the Dap Kinase Architecture

De Diego, I., Kuper, J., Lehmann, F., Wilmanns, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.9 kDa 
• Atom Count: 7,346 
• Modeled Residue Count: 893 
• Deposited Residue Count: 1,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEATH-ASSOCIATED PROTEIN KINASE 1	A, B, C, D	285	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.312 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.94	α = 90
b = 73.7	β = 101.24
c = 120.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): de Diego, I., Lehmann, F., Wilmanns, M.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description