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- PDB-6dd4: Crystal Structure of the Human vaccinia-related kinase bound to a... -

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Basic information

Entry
Database: PDB / ID: 6dd4
TitleCrystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-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-G6J / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsdos Reis, C.V. / Santiago, A.S. / de Souza, G.P. / Counago, R.M. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Massirer, K.B. ...dos Reis, C.V. / Santiago, A.S. / 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,N-dipropyl-dihydropteridine inhibitor
Authors: dos Reis, C.V. / Santiago, A.S. / 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. / ...Authors: dos Reis, C.V. / Santiago, A.S. / 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
DepositionMay 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 16, 2020Group: Database references / Other / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_SG_project / pdbx_database_status
Item: _pdbx_database_status.SG_entry
Revision 1.3Oct 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

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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)166,79329
Polymers164,5534
Non-polymers2,24025
Water4,125229
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4939
Polymers41,1381
Non-polymers3548
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)42,0288
Polymers41,1381
Non-polymers8907
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)41,4566
Polymers41,1381
Non-polymers3185
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)41,8166
Polymers41,1381
Non-polymers6785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.596, 96.168, 191.871
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)
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 254 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-G6J / (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-dipropyl-7,8-dihydropteridin-6(5H)-one


Mass: 391.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23F2N5O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 27.5% PEG3350, 200 mM LiSO4, 0.1M SBG, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.1→33.96 Å / Num. obs: 99522 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.066 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.157 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4898 / CC1/2: 0.687 / Rpim(I) all: 0.736 / % possible all: 100

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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: 2.1→33.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.567 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22555 5033 5.1 %RANDOM
Rwork0.19463 ---
obs0.19622 94402 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2--1.55 Å20 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.1→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9855 0 134 229 10218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910266
X-RAY DIFFRACTIONr_bond_other_d0.0030.029375
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.97213918
X-RAY DIFFRACTIONr_angle_other_deg0.9872.99321663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39451256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13423.625469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76151681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0081566
X-RAY DIFFRACTIONr_chiral_restr0.0890.21490
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111457
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022125
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_it0.8972.265036
X-RAY DIFFRACTIONr_mcbond_other0.8812.255026
X-RAY DIFFRACTIONr_mcangle_it1.4763.3656270
X-RAY DIFFRACTIONr_mcangle_other1.4763.3666271
X-RAY DIFFRACTIONr_scbond_it1.032.355230
X-RAY DIFFRACTIONr_scbond_other1.0292.355230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6093.4957645
X-RAY DIFFRACTIONr_long_range_B_refined3.74626.10311460
X-RAY DIFFRACTIONr_long_range_B_other3.74626.10611461
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 359 -
Rwork0.288 6898 -
obs--99.96 %
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)
11.032-0.3306-1.05881.0441.26133.06350.06590.08660.095-0.0335-0.0567-0.0357-0.2316-0.1044-0.00910.15880.02560.01440.26360.0130.020418.96042.134920.9695
22.15710.48930.09161.9916-0.4032.657-0.06130.14040.0195-0.16180.08060.37990.084-0.3668-0.01930.092-0.0244-0.01780.3017-0.00830.0786-15.82062.340952.1703
31.2499-0.01810.75260.974-0.44952.8609-0.02610.0255-0.07810.1123-0.01620.14350.1768-0.30660.04230.0461-0.0580.03310.3027-0.0180.0369-25.1893-45.297727.2812
41.92120.1625-0.27521.7197-0.07173.4821-0.0118-0.11550.36960.14980.1426-0.0882-0.3135-0.1531-0.13080.04180.0212-0.00640.2444-0.00320.0845-25.5377-9.6642-2.9084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 341
2X-RAY DIFFRACTION2B23 - 600
3X-RAY DIFFRACTION3C21 - 341
4X-RAY DIFFRACTION4D22 - 600

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