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- PDB-6btw: Crystal Structure of the Human vaccinia-related kinase bound to a... -

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Basic information

Entry
Database: PDB / ID: 6btw
TitleCrystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


histone H2AX kinase activity / Cajal body organization / Golgi disassembly / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / nucleosomal DNA binding ...histone H2AX kinase activity / Cajal body organization / Golgi disassembly / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / nucleosomal DNA binding / Cajal body / neuron projection development / kinase activity / protein autophosphorylation / histone binding / 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 kinase activity / protein phosphorylation / chromatin remodeling / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein kinase binding / nucleolus / chromatin / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-E8D / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCounago, R.M. / dos Reis, C.V. / de Souza, G.P. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. ...Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.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 the Human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor
Authors: Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / ...Authors: Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC)
History
DepositionDec 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase VRK1
B: Serine/threonine-protein kinase VRK1
C: Serine/threonine-protein kinase VRK1
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,26019
Polymers164,5534
Non-polymers1,70715
Water17,637979
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5784
Polymers41,1381
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6145
Polymers41,1381
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4545
Polymers41,1381
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6145
Polymers41,1381
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.576, 97.562, 193.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1


Mass: 41138.125 Da / Num. of mol.: 4 / Fragment: residues 3-364
Mutation: K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Details (production host): pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 994 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-E8D / 2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one


Mass: 369.325 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H13F2N5O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 979 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→19.89 Å / Num. obs: 137864 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.092 / Rrim(I) all: 0.166 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.512 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.698 / Rpim(I) all: 0.966 / Rrim(I) all: 1.798 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP5

3op5


Resolution: 1.9→19.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.331 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 6723 4.9 %RANDOM
Rwork0.18197 ---
obs0.18357 131052 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--1.64 Å2-0 Å2
3----1.76 Å2
Refinement stepCycle: 1 / Resolution: 1.9→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9787 0 107 979 10873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910176
X-RAY DIFFRACTIONr_bond_other_d0.0020.029285
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.96713804
X-RAY DIFFRACTIONr_angle_other_deg0.952.99521452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06951239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.2723.562466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.987151673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1311568
X-RAY DIFFRACTIONr_chiral_restr0.0870.21473
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022142
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_it2.0182.9074965
X-RAY DIFFRACTIONr_mcbond_other2.0152.9064964
X-RAY DIFFRACTIONr_mcangle_it2.9714.3386189
X-RAY DIFFRACTIONr_mcangle_other2.9714.3386190
X-RAY DIFFRACTIONr_scbond_it2.4913.0665211
X-RAY DIFFRACTIONr_scbond_other2.4913.0665211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8664.5217612
X-RAY DIFFRACTIONr_long_range_B_refined5.61233.94811982
X-RAY DIFFRACTIONr_long_range_B_other5.61233.9511983
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 481 -
Rwork0.277 9624 -
obs--99.69 %

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