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- PDB-9fet: Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) boun... -

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Basic information

Entry
Database: PDB / ID: 9fet
TitleCrystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-47
ComponentsSerine/threonine-protein kinase VRK2
KeywordsTRANSFERASE / Kinase / VRK2 / Inhibitor / JA-296
Function / homology
Function and homology information


regulation of interleukin-1-mediated signaling pathway / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / regulation of MAPK cascade / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / mitochondrial membrane ...regulation of interleukin-1-mediated signaling pathway / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / regulation of MAPK cascade / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / mitochondrial membrane / nuclear envelope / cellular response to oxidative stress / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein phosphorylation / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / endoplasmic reticulum membrane / protein kinase binding / endoplasmic reticulum / signal transduction / protein-containing complex / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-REB / Serine/threonine-protein kinase VRK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, G.Q. / Amrhein, J.A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-47
Authors: Wang, G.Q. / Amrhein, J.A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMay 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase VRK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1202
Polymers36,7881
Non-polymers3311
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.675, 71.314, 158.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Serine/threonine-protein kinase VRK2 / Vaccinia-related kinase 2


Mass: 36788.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q86Y07, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-REB / [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile


Mass: 331.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG6000 -- 10% ethylene glycol -- 0.1M tris pH 7.5 -- 0.1M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.918396 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918396 Å / Relative weight: 1
ReflectionResolution: 2.4→44.41 Å / Num. obs: 12986 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1328 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.842 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 660 5.1 %RANDOM
Rwork0.22183 ---
obs0.22421 12325 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.088 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å2-0 Å2-0 Å2
2--7.33 Å20 Å2
3----4.78 Å2
Refinement stepCycle: 1 / Resolution: 2.4→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 25 10 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162342
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.643407
X-RAY DIFFRACTIONr_angle_other_deg1.2741.5925388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1945312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14422.966118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2461511
X-RAY DIFFRACTIONr_chiral_restr0.0620.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4846.5411254
X-RAY DIFFRACTIONr_mcbond_other5.486.5391253
X-RAY DIFFRACTIONr_mcangle_it8.2959.8041564
X-RAY DIFFRACTIONr_mcangle_other8.2939.8071565
X-RAY DIFFRACTIONr_scbond_it5.2916.7651260
X-RAY DIFFRACTIONr_scbond_other5.2896.7681261
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1479.9721841
X-RAY DIFFRACTIONr_long_range_B_refined13.15466.810212
X-RAY DIFFRACTIONr_long_range_B_other13.154109.310212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 44 -
Rwork0.365 904 -
obs--99.89 %

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