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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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.