2W4J | pdb_00002w4j

X-ray structure of a DAP-Kinase 2-277

• PDB DOI: https://doi.org/10.2210/pdb2W4J/pdb

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


• Deposited: 2008-11-27 Released: 2009-12-22 
• Deposition Author(s): De Diego, I., Kuper, J., Lehmann, F., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.159 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

X-Ray Structure of a Dap-Kinase Calmodulin Complex

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 32.36 kDa 
• Atom Count: 2,675 
• Modeled Residue Count: 276 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEATH-ASSOCIATED PROTEIN KINASE 1	A	277	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.159 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.844	α = 90
b = 62.336	β = 90
c = 88.345	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: 2009-12-22 
Deposition Author(s): De Diego, I., Kuper, J., Lehmann, F., Wilmanns, M.

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description