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- PDB-4jxf: Crystal Structure of PLK4 Kinase with an inhibitor: 400631 ((1R,2... -

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Basic information

Entry
Database: PDB / ID: 4jxf
TitleCrystal Structure of PLK4 Kinase with an inhibitor: 400631 ((1R,2S)-2-{3-[(E)-2-{4-[(DIMETHYLAMINO)METHYL]PHENYL}ETHENYL]-2H-INDAZOL-6-YL}-5'-METHOXYSPIRO[CYCLOPROPANE-1,3'-INDOL]-2'(1'H)-ONE)
ComponentsSerine/threonine-protein kinase PLK4
Keywordstransferase/transferase inhibitor / Serine/Threonine kinase / Polo-like kinase 4 / inhibitor / Transferase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / centriole replication / cleavage furrow ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / centriole replication / cleavage furrow / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / ATP binding / identical protein binding / cytosol
Similarity search - Function
Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / POLO box domain ...Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / POLO box domain / POLO box domain profile. / Tyrosine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-631 / Serine/threonine-protein kinase PLK4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsQiu, W. / Plotnikova, O. / Feher, M. / Awrey, D.E. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal Structure of PLK4 Kinase with an inhibitor: 400631
Authors: Qiu, W. / Plotnikova, O. / Feher, M. / Awrey, D.E. / Chirgadze, N.Y.
History
DepositionMar 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1054
Polymers30,5161
Non-polymers5893
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.571, 127.571, 127.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak


Mass: 30516.379 Da / Num. of mol.: 1 / Fragment: PLK4 kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Production host: Escherichia coli (E. coli) / References: UniProt: O00444, polo kinase
#2: Chemical ChemComp-631 / (1R,2S)-2-{3-[(E)-2-{4-[(dimethylamino)methyl]phenyl}ethenyl]-2H-indazol-6-yl}-5'-methoxyspiro[cyclopropane-1,3'-indol]-2'(1'H)-one


Mass: 464.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H28N4O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% PEG 3350, 0.1 M HEPES pH 7.5 0.16 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 28, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 13619 / Num. obs: 13604 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.37 % / Biso Wilson estimate: 61.66 Å2 / Rmerge(I) obs: 0.1077 / Net I/σ(I): 27.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 19.08 % / Rmerge(I) obs: 0.7625 / Mean I/σ(I) obs: 3.56 / Num. unique all: 1511 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3COK

3cok


Resolution: 2.4→28.53 Å / Cor.coef. Fo:Fc: 0.9009 / Cor.coef. Fo:Fc free: 0.8868 / SU R Cruickshank DPI: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 672 4.96 %RANDOM
Rwork0.2539 ---
obs0.2546 13553 99.33 %-
all-13604 --
Displacement parametersBiso mean: 54.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.434 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 43 56 1999
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081993HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972684HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d936SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it1993HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion3.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion248SEMIHARMONIC5
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_contact2201SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.59 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2764 142 5.23 %
Rwork0.2592 2572 -
all0.2601 2714 -
obs--99.33 %

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