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- PDB-6ncg: Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) boun... -

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Basic information

Entry
Database: PDB / ID: 6ncg
TitleCrystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to pyridin-benzenesulfonamide inhibitor
ComponentsSerine/threonine-protein kinase VRK2
KeywordsTRANSFERASE / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
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 / non-specific serine/threonine protein kinase / protein phosphorylation / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein kinase binding / signal transduction / endoplasmic reticulum / protein-containing complex / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KJD / Serine/threonine-protein kinase VRK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
Authorsdos Reis, C.V. / Chiodi, C.G. / de Souza, G.P. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Counago, R.M. / Massirer, K.B. / Elkins, J.M. ...dos Reis, C.V. / Chiodi, C.G. / de Souza, G.P. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Counago, R.M. / Massirer, K.B. / Elkins, J.M. / Arruda, P. / Edwards, A.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to pyridin-benzenesulfonamide inhibitor
Authors: dos Reis, C.V. / Chiodi, C.G. / de Souza, G.P. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Counago, R.M. / Massirer, K.B. / Arruda, P. / Elkins, J.M. / ...Authors: dos Reis, C.V. / Chiodi, C.G. / de Souza, G.P. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Counago, R.M. / Massirer, K.B. / Arruda, P. / Elkins, J.M. / Edwards, A.M. / Structural Genomics Consortium (SGC)
History
DepositionDec 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,4275
Polymers73,5762
Non-polymers8513
Water73941
1
A: Serine/threonine-protein kinase VRK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2623
Polymers36,7881
Non-polymers4732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase VRK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1662
Polymers36,7881
Non-polymers3771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.528, 67.625, 171.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36788.230 Da / Num. of mol.: 2 / Fragment: residues 14-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86Y07, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-KJD / 4-[6-amino-5-(3,5-difluoro-4-hydroxyphenyl)pyridin-3-yl]benzene-1-sulfonamide


Mass: 377.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13F2N3O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 27.5% PEG3350; 200 mM LiSO4; 0.1M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→29.1 Å / Num. obs: 24095 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.061 / Rrim(I) all: 0.15 / Net I/σ(I): 10.8
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.773 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2679 / CC1/2: 0.707 / Rpim(I) all: 0.824 / Rrim(I) all: 1.96 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UU1

5uu1


Resolution: 2.45→29.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.908 / SU B: 19.89 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R: 0.553 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29694 1241 5.2 %RANDOM
Rwork0.22061 ---
obs0.22443 22794 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.063 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å20 Å20 Å2
2--11.7 Å2-0 Å2
3----7.08 Å2
Refinement stepCycle: 1 / Resolution: 2.45→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 57 41 4564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194631
X-RAY DIFFRACTIONr_bond_other_d0.0010.024116
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9656305
X-RAY DIFFRACTIONr_angle_other_deg0.7792.9959466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0435586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.99624.022184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57515683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4011520
X-RAY DIFFRACTIONr_chiral_restr0.0620.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02943
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_it3.9256.9182374
X-RAY DIFFRACTIONr_mcbond_other3.9256.9172373
X-RAY DIFFRACTIONr_mcangle_it6.33710.3472950
X-RAY DIFFRACTIONr_mcangle_other6.33610.3492951
X-RAY DIFFRACTIONr_scbond_it3.86.9822257
X-RAY DIFFRACTIONr_scbond_other3.86.9622254
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.08610.373350
X-RAY DIFFRACTIONr_long_range_B_refined11.29918759
X-RAY DIFFRACTIONr_long_range_B_other11.29818760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 81 -
Rwork0.368 1680 -
obs--99.89 %

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