9FET | pdb_00009fet

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.269 (Depositor), 0.262 (DCC)
R-Value Work:
0.222 (Depositor), 0.227 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86Y07
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
REB (Subject of Investigation/LOI) Query on REB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile C₁₈ H₁₇ N₇ YRRRHSNOXWKVDL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.269 (Depositor), 0.262 (DCC)
R-Value Work: 0.222 (Depositor), 0.227 (DCC)
R-Value Observed: 0.224 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Structural Genomics Consortium (SGC)

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.