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- PDB-6vxu: Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471 -

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Basic information

Entry
Database: PDB / ID: 6vxu
TitleStructure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding ...Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol
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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-RTJ / Chem-VBD / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsdos Reis, C.V. / Dutra, L.A. / Gama, F.H. / Mascarello, A. / Azevedo, H. / Guimaraes, C.R. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Counago, R.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/50724-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)465651/2014-3 Brazil
Sao Paulo Research Foundation (FAPESP)2014/50897-0 Brazil
CitationJournal: To Be Published
Title: Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471
Authors: Guimaraes, C.R. / Counago, R.M.
History
DepositionFeb 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 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)167,58723
Polymers164,5534
Non-polymers3,03519
Water10,629590
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7304
Polymers41,1381
Non-polymers5923
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)41,8265
Polymers41,1381
Non-polymers6884
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)41,9186
Polymers41,1381
Non-polymers7805
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)42,1148
Polymers41,1381
Non-polymers9767
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.771, 96.300, 191.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
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)
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 609 molecules

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


Mass: 399.394 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H19F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-VBD / (7S)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one


Mass: 399.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27.5% PEG3350; 300 mM LiSO4; 0.1 M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2019
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→48.15 Å / Num. obs: 112736 / % possible obs: 97.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.944 / Num. unique obs: 4515 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BRU

6bru


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.419 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5597 5 %RANDOM
Rwork0.184 ---
obs0.185 107011 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.71 Å2 / Biso mean: 39.26 Å2 / Biso min: 21.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9743 0 192 590 10525
Biso mean--64.53 47.08 -
Num. residues----1251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01310182
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179150
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.64213851
X-RAY DIFFRACTIONr_angle_other_deg1.2661.57821108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31651243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36421.877522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.834151588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9081563
X-RAY DIFFRACTIONr_chiral_restr0.0620.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022179
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 358 -
Rwork0.284 6486 -
all-6844 -
obs--81.21 %
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)
10.9292-0.2586-1.05520.99481.07212.96710.08490.04790.08220.0129-0.0762-0.0261-0.1779-0.0999-0.00860.06790.02360.00290.18990.00010.014819.43812.388421.0161
21.89030.40430.05932.0559-0.37042.412-0.05650.08150.0306-0.15470.08560.36470.0303-0.3455-0.02910.0792-0.0123-0.00160.2348-0.01170.0775-15.61542.588152.2975
31.0419-0.06440.84630.7403-0.43272.8895-0.0219-0.0258-0.08060.1122-0.00880.08960.1462-0.25180.03070.042-0.03560.02940.2126-0.00510.0263-25.4191-45.56627.3216
41.95240.1674-0.54191.54510.5252.3390.0058-0.06880.32660.03040.0453-0.0806-0.18590.0011-0.05110.020.0023-0.00930.17970.00380.068-25.6309-9.7867-2.8866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 600
2X-RAY DIFFRACTION2B23 - 600
3X-RAY DIFFRACTION3C21 - 600
4X-RAY DIFFRACTION4D22 - 600

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