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- PDB-5ukf: Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to... -

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Basic information

Entry
Database: PDB / ID: 5ukf
TitleCrystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole 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-8E1 / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCounago, R.M. / Wells, C. / Zuercher, W. / Willson, T.M. / Bountra, C. / Edwards, A.M. / Arruda, P. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: Sci Rep / Year: 2017
Title: Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Authors: Counago, R.M. / Allerston, C.K. / Savitsky, P. / Azevedo, H. / Godoi, P.H. / Wells, C.I. / Mascarello, A. / de Souza Gama, F.H. / Massirer, K.B. / Zuercher, W.J. / Guimaraes, C.R.W. / Gileadi, O.
History
DepositionJan 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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)166,71323
Polymers164,2044
Non-polymers2,50919
Water9,926551
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5544
Polymers41,0511
Non-polymers5033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8397
Polymers41,0511
Non-polymers7886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6495
Polymers41,0511
Non-polymers5984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6717
Polymers41,0511
Non-polymers6206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.138, 96.051, 192.741
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: 41051.047 Da / Num. of mol.: 4 / Fragment: UNP residues 3-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / 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, 570 molecules

#2: Chemical
ChemComp-8E1 / 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide


Mass: 372.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H12N4O3S2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 27.5% PEG 3350; 0.3M AmSO4; 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2016
Details: Kirkpatrick Baez (KB) bimorph mirror pair for horizontal and vertical focussing
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→29.56 Å / Num. obs: 67658 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 53.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.028 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4493 / CC1/2: 0.807 / Rpim(I) all: 0.352 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP5

3op5


Resolution: 2.4→24.19 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3415 5.06 %RANDOM
Rwork0.177 ---
obs0.179 67552 100 %-
Displacement parametersBiso mean: 60.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.9223 Å20 Å20 Å2
2---9.5099 Å20 Å2
3---7.5875 Å2
Refinement stepCycle: 1 / Resolution: 2.4→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9154 0 149 551 9854
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019517HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0812926HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3196SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes211HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1388HARMONIC5
X-RAY DIFFRACTIONt_it9517HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion17.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1198SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10996SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2136 226 4.57 %
Rwork0.2003 4716 -
all0.201 4942 -
obs--100 %
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)
17.1230.2686-2.04144.55181.51710.83870.04030.4599-0.439-0.23310.4105-0.62580.72260.8567-0.4508-0.13340.0715-0.09060.1156-0.1107-0.163480.80752.52791.3548
22.1958-0.35680.29582.18061.75013.44430.1529-0.1303-0.0590.2326-0.0366-0.22810.390.0548-0.1163-0.11220.0005-0.0452-0.0697-0.0153-0.24868.31113.883788.0726
32.67720.03341.3151.69630.54222.6910.31390.0752-0.18050.21190.0341-0.56480.77160.5021-0.3480.0430.1345-0.0766-0.011-0.0058-0.156273.8428-5.971679.4281
41.43430.41660.85414.06762.14415.31380.1435-0.2404-0.12010.2797-0.0945-0.12320.5658-0.1902-0.049-0.0286-0.0289-0.0586-0.0299-0.0345-0.210261.4249-3.546777.755
51.7472-0.8358-0.12652.81051.4645.0144-0.002-0.03650.1252-0.26480.0158-0.1625-0.3887-0.0284-0.0138-0.0486-0.0211-0.0333-0.0702-0.04-0.247660.84182.501665.5235
62.28721.4411.10834.5827-0.3586.117-0.08890.1818-0.0307-0.37820.2364-0.48050.12570.6075-0.14750.0505-0.00180.0329-0.144-0.0876-0.301664.6033-5.146454.0854
70.4124-0.17770.64954.9091.74066.08350.0095-0.1518-0.20190.1441-0.34680.43380.9314-0.78620.3373-0.0184-0.1734-0.04440.0584-0.0937-0.160851.8145-10.921866.9945
87.9778-0.18-2.33896.99480.40792.9526-0.2107-0.4674-0.50760.58320.52430.7920.5727-0.521-0.3136-0.1326-0.09780.06680.00810.2204-0.195427.9477-11.404652.9311
90.0057-2.43630.28583.3855-0.69490-0.1602-0.7046-0.19370.55430.38380.4610.2777-0.5237-0.22360.0114-0.02720.15580.1290.0719-0.147324.5398-9.023354.8845
102.5138-1.1979-2.19264.5523-1.18670.5245-0.0803-0.44410.23380.0666-0.20390.5951-0.3603-0.69540.2843-0.10360.147-0.03950.1009-0.09510.032121.34798.037541.7002
112.0909-0.43420.34411.9089-0.22242.5759-0.0189-0.18710.01860.0417-0.02620.33160.0366-0.40640.0451-0.114-0.0115-0.0261-0.1079-0.0175-0.189234.3746-3.317241.2311
124.08780.6440.69211.77061.45043.4474-0.1760.65150.3889-0.31050.02280.1828-0.3638-0.07810.15320.02950.0453-0.0598-0.12190.0658-0.175934.79732.40423.8275
131.757-0.23840.75881.38870.06363.2594-0.1618-0.03690.53380.0148-0.0160.0638-0.6039-0.13510.17780.03980.0042-0.0443-0.1108-0.0292-0.066241.69679.46740.8151
142.58781.0482-0.8127.4844.35593.8246-0.0253-0.01680.8730.3428-0.07270.472-0.9843-0.22160.09790.34260.16990.0424-0.25640.0544-0.199527.415862.087151.8561
152.9107-0.3027-1.94760.436-0.27763.80430.11580.15710.2486-0.2087-0.01860.137-0.4774-0.5214-0.0972-0.03830.0777-0.0161-0.09350.0279-0.230322.136948.324561.7207
164.5595-0.86793.04150-2.17536.04010.02120.02260.58670.23220.053-0.4178-0.12920.5444-0.0742-0.1010.00820.14880.09840.0979-0.142835.294240.865176.919
171.8002-0.0453-0.88331.1192-0.20693.6969-0.1174-0.044-0.01830.0084-0.00330.28020.0088-0.57350.1208-0.1987-0.01060.0374-0.03170.0056-0.212214.123339.021679.8654
186.79020.40950.20833.56131.65110.5923-0.05830.6034-0.7022-0.5340.31740.50580.3136-0.2804-0.2591-0.1006-0.1116-0.1223-0.0812-0.0735-0.067510.52255.043989.2316
193.4362-0.71860.05963.4017-0.01863.95880.28210.9701-0.529-0.7534-0.03970.10040.1129-0.2955-0.2424-0.0965-0.0031-0.09730.0075-0.1385-0.033514.50526.682886.4225
200.40833.5734-0.32913.7123.10620.5896-0.10480.167-0.6689-0.1992-0.0687-0.26920.44650.27010.1735-0.1240.10370.011-0.0257-0.04270.049831.04821.378298.8395
212.34320.78810.13110.5046-0.41081.581-0.06480.0803-0.1516-0.17170.0823-0.0544-0.15570.2444-0.0176-0.1168-0.03810.00810.0503-0.0279-0.102125.292415.877193.7575
222.082-0.32580.02481.6560.04821.8046-0.0397-0.0437-0.29820.01760.05460.14850.1384-0.0141-0.0149-0.1729-0.01370.0087-0.04850.0167-0.118317.137113.1428102.936
234.1742.051-0.96670.0009-1.38831.8337-0.0247-0.5414-0.2470.5763-0.097-0.23050.02080.2360.1218-0.05850.0575-0.02910.1550.0502-0.048626.151913.8533118.005
242.2223-2.33020.46255.0020.0532.1888-0.0551-0.06690.2362-0.0012-0.1421-0.4586-0.16160.24410.1972-0.0772-0.0008-0.10010.2452-0.01570.095737.932719.9352111.363
255.16491.6796-0.19392.8921-0.44861.5347-0.05460.0650.33320.14930.0734-0.06890.0444-0.0276-0.0188-0.128-0.0238-0.0202-0.0624-0.0161-0.167123.663926.0216103.682
265.2209-0.407-0.78734.62432.51595.34260.07920.22260.0398-0.25780.129-0.5343-0.34450.6633-0.2082-0.1852-0.08520.0630.0988-0.0266-0.135833.525919.780592.2526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|20 - 56}
2X-RAY DIFFRACTION2{A|57 - 121}
3X-RAY DIFFRACTION3{A|122 - 150}
4X-RAY DIFFRACTION4{A|151 - 205}
5X-RAY DIFFRACTION5{A|206 - 256}
6X-RAY DIFFRACTION6{A|257 - 280}
7X-RAY DIFFRACTION7{A|281 - 341}
8X-RAY DIFFRACTION8{B|51 - 103}
9X-RAY DIFFRACTION9{B|104 - 131}
10X-RAY DIFFRACTION10{B|132 - 150}
11X-RAY DIFFRACTION11{B|151 - 256}
12X-RAY DIFFRACTION12{B|257 - 280}
13X-RAY DIFFRACTION13{B|281 - 341}
14X-RAY DIFFRACTION14{C|21 - 56}
15X-RAY DIFFRACTION15{C|57 - 205}
16X-RAY DIFFRACTION16{C|206 - 223}
17X-RAY DIFFRACTION17{C|224 - 341}
18X-RAY DIFFRACTION18{D|39 - 102}
19X-RAY DIFFRACTION19{D|103 - 132}
20X-RAY DIFFRACTION20{D|133 - 150}
21X-RAY DIFFRACTION21{D|151 - 170}
22X-RAY DIFFRACTION22{D|171 - 256}
23X-RAY DIFFRACTION23{D|257 - 280}
24X-RAY DIFFRACTION24{D|281 - 296}
25X-RAY DIFFRACTION25{D|297 - 316}
26X-RAY DIFFRACTION26{D|317 - 341}

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