9FET

Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-47

• PDB DOI: https://doi.org/10.2210/pdb9FET/pdb

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


• Deposited: 2024-05-21 Released: 2024-09-11 
• Deposition Author(s): Wang, G.Q., Amrhein, J.A., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): The Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-47

Wang, G.Q., Amrhein, J.A., Knapp, S., Structural Genomics Consortium (SGC)

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.12 kDa 
• Atom Count: 2,458 
• Modelled Residue Count: 313 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase VRK2	A	324	Homo sapiens	Mutation(s): 0  Gene Names: VRK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86Y07 (Homo sapiens) Explore Q86Y07  Go to UniProtKB:  Q86Y07
PHAROS:  Q86Y07 GTEx:  ENSG00000028116

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
REB (Subject of Investigation/LOI)	B [auth A]	[4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile C18 H17 N7 YRRRHSNOXWKVDL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.675	α = 90
b = 71.314	β = 90
c = 158.718	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Wang, G.Q., Amrhein, J.A., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
The Structural Genomics Consortium (SGC)	Canada	--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release