5O26 | pdb_00005o26

Crystal structure of WNK3 kinase domain in a diphosphorylated state and in complex with AMP-PNP/Mg2+

• PDB DOI: https://doi.org/10.2210/pdb5O26/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-05-19 Released: 2017-06-28 
• Deposition Author(s): Pinkas, D.M., Bufton, J.C., Newman, J.A., Kopec, J., Borkowska, O., Chalk, R., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.278 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Crystal structure of WNK3 kinase domain in a diphosphorylated state and in complex with AMP-PNP/Mg2+

Pinkas, D.M., Daubner, G.M., Bufton, J.C., Bartual, S.G., Sanvitale, C.E., Alessi, D.R., Bullock, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.54 kDa 
• Atom Count: 4,489 
• Modeled Residue Count: 540 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase WNK3	A, B	284	Homo sapiens	Mutation(s): 0  Gene Names: WNK3, KIAA1566, PRKWNK3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYP7 (Homo sapiens) Explore Q9BYP7  Go to UniProtKB:  Q9BYP7
PHAROS:  Q9BYP7 GTEx:  ENSG00000196632

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A], G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	D [auth A], E [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.278 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.163	α = 79.79
b = 56.4	β = 80.73
c = 71.236	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Pinkas, D.M., Bufton, J.C., Newman, J.A., Kopec, J., Borkowska, O., Chalk, R., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 2.0: 2018-10-31
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2019-10-16
  Changes: Data collection
• Version 2.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary