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

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Basic information

Entry
Database: PDB / ID: 6cqh
TitleCrystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-dihydropteridine 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 / histone H3T3 kinase activity / 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 ...histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / 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 / histone H3S10 kinase activity / Cajal body / nucleosomal DNA binding / neuron projection development / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol
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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / 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, 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
ACETATE ION / Chem-F8Y / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
Authorsdos Reis, C.V. / de Souza, G.P. / Counago, R.M. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. ...dos Reis, C.V. / de Souza, G.P. / Counago, R.M. / 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 N-propynyl-N-ethyl-dihydropteridine inhibitor
Authors: dos Reis, C.V. / de Souza, G.P. / Counago, R.M. / Azevedo, H. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / ...Authors: dos Reis, C.V. / de Souza, G.P. / Counago, R.M. / 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
DepositionMar 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: 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
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 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)166,98524
Polymers164,5534
Non-polymers2,43320
Water11,602644
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8556
Polymers41,1381
Non-polymers7175
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)41,8717
Polymers41,1381
Non-polymers7326
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)41,4264
Polymers41,1381
Non-polymers2883
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)41,8347
Polymers41,1381
Non-polymers6956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.492, 96.560, 193.395
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 664 molecules

#2: Chemical ChemComp-F8Y / (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-ethyl-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one


Mass: 373.357 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H17F2N5O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.96862 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.15→29.67 Å / Num. obs: 94709 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.128 / Rrim(I) all: 0.223 / Net I/σ(I): 6.5
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4626 / CC1/2: 0.634 / Rpim(I) all: 0.732 / Rrim(I) all: 1.262 / % possible all: 99.9

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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: 2.15→29.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.168 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23885 4834 5.1 %RANDOM
Rwork0.20065 ---
obs0.2026 89796 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.416 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0 Å2
2---0.17 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.15→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9842 0 149 644 10635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910327
X-RAY DIFFRACTIONr_bond_other_d0.0020.029373
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.97214029
X-RAY DIFFRACTIONr_angle_other_deg0.9482.99321665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08751271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74623.561469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.188151685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8661567
X-RAY DIFFRACTIONr_chiral_restr0.0770.21499
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022146
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_it0.4570.9495065
X-RAY DIFFRACTIONr_mcbond_other0.4550.9475062
X-RAY DIFFRACTIONr_mcangle_it0.8581.4196329
X-RAY DIFFRACTIONr_mcangle_other0.8581.4196330
X-RAY DIFFRACTIONr_scbond_it0.2720.9995262
X-RAY DIFFRACTIONr_scbond_other0.2720.9995262
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4521.4987697
X-RAY DIFFRACTIONr_long_range_B_refined4.14811.46311685
X-RAY DIFFRACTIONr_long_range_B_other4.14811.46611686
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 371 -
Rwork0.274 6547 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.38121.11880.58036.32011.33475.05430.0633-0.01240.35170.10960.0096-0.4712-0.27710.0438-0.07280.11810.0230.04340.31240.0040.107634.7958-1.54163.9883
20.9843-0.7765-0.78493.00481.12681.91030.11610.15940.0391-0.2122-0.1102-0.0806-0.1621-0.1487-0.00590.16470.03420.00920.3230.00380.003819.16240.522315.5574
30.31030.02420.63864.5751-2.44242.68260.33140.0744-0.34940.2456-0.1102-1.01150.50520.2346-0.22110.6767-0.0325-0.20540.381-0.05590.788114.4257-14.144832.2921
40.5479-0.0533-0.11462.3122-0.0153.2360.0221-0.03010.12270.2772-0.0224-0.0812-0.11740.0470.00030.21910.01960.01110.2672-0.03390.034616.02274.907837.2118
50.668-0.5242-0.53065.53-1.13233.19040.0362-0.01610.1938-0.0949-0.09280.3912-0.3058-0.39910.05650.19310.0967-0.01440.3996-0.08460.18125.233610.619227.0507
62.12591.9993-1.7648.2547-1.15573.31890.21940.06120.29580.3393-0.16850.7839-0.463-0.3946-0.05090.33530.024-0.12580.53410.08530.5764-35.452516.733443.3929
74.3129-0.74420.10844.0824-0.17681.4327-0.05830.08740.3928-0.10240.20570.4813-0.2598-0.1965-0.14740.2359-0.0164-0.05130.37740.02290.1827-23.863911.743844.0331
81.3069-0.05040.1481.9671-0.25582.47940.0049-0.0314-0.03440.0795-0.00010.21210.0224-0.2165-0.00480.116-0.0020.00840.2878-0.02260.0366-13.32221.392457.9815
99.55785.6019-0.24547.95080.35194.08870.0014-0.3097-0.17360.27810.00950.09410.27130.0324-0.01090.25120.03180.00810.27560.05360.2134-5.2182-11.004568.7263
101.00511.12490.51754.62240.57982.1157-0.0780.0411-0.2132-0.4063-0.00160.01870.3591-0.00540.07970.25770.03250.03210.2954-0.01480.0906-4.5662-8.119751.7261
114.8831.97471.61746.54632.22075.4090.03390.1664-0.70950.0716-0.0061-0.14040.7152-0.038-0.02780.42-0.0376-0.02860.27850.05110.1427-18.5906-62.523446.0252
122.9607-0.41961.22161.214-0.65772.6127-0.0054-0.1465-0.14270.19180.01810.02770.1573-0.1877-0.01260.1387-0.03670.00310.28280.00850.0085-23.4342-47.317733.5457
1341.7199-33.128368.01771.6781-6.7078160.57580.5730.4451-0.3189-0.19460.6391-0.48581.24321.735-1.2120.35180.12570.0150.50060.05590.3565-18.3495-49.548515.823
142.65350.6249-0.09341.125-0.42943.0556-0.05530.1788-0.3177-0.0873-0.0289-0.00940.2458-0.19210.08420.083-0.0136-0.00450.3116-0.00290.0524-27.6799-45.02313.0919
153.36860.13640.72720.923-0.08641.895-0.1768-0.04730.22670.02520.06680.2289-0.187-0.27280.110.14280.045-0.04920.34330.01820.0983-35.3665-34.505419.1181
164.18652.3842-4.89285.9175-5.79957.71910.21950.66940.08530.0327-0.01620.1705-0.244-0.5576-0.20330.47940.03810.02310.5156-0.02390.6151-40.325215.17243.7924
173.7152-0.6308-0.07763.84970.61571.96320.049-0.12520.597-0.04160.07650.189-0.4394-0.173-0.12560.15570.01380.04780.3452-0.05340.1949-36.7493-0.51766.5171
182.20710.1995-0.52761.46340.26492.03320.0029-0.00580.2249-0.04830.0705-0.0301-0.11980.0747-0.07340.02680.00580.00220.26090.00430.025-24.9865-12.3686-7.1177
197.88812.23291.06353.32330.04081.58670.00260.0828-0.2119-0.0566-0.01-0.10080.05580.07990.00740.2120.01450.03820.2682-0.01410.2316-11.8708-20.7102-17.1732
204.97010.46830.94170.69560.36812.1502-0.052-0.427-0.09630.08970.0595-0.26080.18250.2556-0.00750.10580.0885-0.00690.35050.01580.1125-17.318-22.5994-1.795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 71
2X-RAY DIFFRACTION2A72 - 210
3X-RAY DIFFRACTION3A211 - 222
4X-RAY DIFFRACTION4A223 - 290
5X-RAY DIFFRACTION5A291 - 341
6X-RAY DIFFRACTION6B23 - 43
7X-RAY DIFFRACTION7B50 - 137
8X-RAY DIFFRACTION8B138 - 276
9X-RAY DIFFRACTION9B277 - 294
10X-RAY DIFFRACTION10B295 - 341
11X-RAY DIFFRACTION11C21 - 59
12X-RAY DIFFRACTION12C60 - 214
13X-RAY DIFFRACTION13C215 - 222
14X-RAY DIFFRACTION14C223 - 276
15X-RAY DIFFRACTION15C277 - 341
16X-RAY DIFFRACTION16D22 - 28
17X-RAY DIFFRACTION17D29 - 134
18X-RAY DIFFRACTION18D135 - 276
19X-RAY DIFFRACTION19D277 - 294
20X-RAY DIFFRACTION20D295 - 341

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