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- PDB-8q1z: Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) boun... -

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Basic information

Entry
Database: PDB / ID: 8q1z
TitleCrystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-296
ComponentsSerine/threonine-protein kinase VRK2
KeywordsTRANSFERASE / inhibitor / kinase / VRK2
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-IKD / Serine/threonine-protein kinase VRK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, G.Q. / Amrhein, J.A. / Knapp, S.
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-296
Authors: Wang, G.Q. / Amrhein, J.A. / Knapp, S.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: 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)37,1362
Polymers36,7881
Non-polymers3471
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.732, 71.031, 158.030
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
Details: LIG is the compound that reversibly binds to VRK2 / 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-IKD / 2-[4-[[4-[(3-~{tert}-butyl-1~{H}-pyrazol-5-yl)amino]pyrimidin-2-yl]amino]phenyl]ethanenitrile


Mass: 347.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H21N7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 -- 0.2M potassium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9183962 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183962 Å / Relative weight: 1
ReflectionResolution: 1.85→44.37 Å / Num. obs: 27769 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 14.5
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 1677 / CC1/2: 0.551

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→44.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.359 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25075 1392 5 %RANDOM
Rwork0.19992 ---
obs0.20257 26375 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.814 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--2.1 Å2-0 Å2
3----2.04 Å2
Refinement stepCycle: 1 / Resolution: 1.85→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 26 121 2543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122486
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162286
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.6473379
X-RAY DIFFRACTIONr_angle_other_deg0.4671.5685249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.452510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68810382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
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_it2.9613.4121244
X-RAY DIFFRACTIONr_mcbond_other2.9613.4121244
X-RAY DIFFRACTIONr_mcangle_it4.3256.1091552
X-RAY DIFFRACTIONr_mcangle_other4.3246.1111553
X-RAY DIFFRACTIONr_scbond_it3.6343.6381242
X-RAY DIFFRACTIONr_scbond_other3.6333.6391243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.556.5661827
X-RAY DIFFRACTIONr_long_range_B_refined7.41533.222896
X-RAY DIFFRACTIONr_long_range_B_other7.39933.032878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.897 Å
RfactorNum. reflection% reflection
Rfree0.345 111 -
Rwork0.332 1911 -
obs--99.21 %

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