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- PDB-3db6: Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (... -

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Basic information

Entry
Database: PDB / ID: 3db6
TitleCrystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 902
ComponentsPolo-like kinase 1
KeywordsTRANSFERASE / Polo-like kinase 1 / Plk1 / catalytic domain / small-molecule inhibitor / Kinase
Function / homology
Function and homology information


Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / EML4 and NUDC in mitotic spindle formation / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / The role of GTSE1 in G2/M progression after G2 checkpoint ...Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / EML4 and NUDC in mitotic spindle formation / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / The role of GTSE1 in G2/M progression after G2 checkpoint / polo kinase / mitotic spindle organization / kinetochore / spindle pole / retina development in camera-type eye / mitotic cell cycle / midbody / cell division / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FRS / Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsElling, R.A. / Fucini, R.V. / Zhu, J. / Barr, K.J. / Romanowski, M.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of the Brachydanio rerio Polo-like kinase 1 (Plk1) catalytic domain in complex with an extended inhibitor targeting the adaptive pocket of the enzyme.
Authors: Elling, R.A. / Fucini, R.V. / Hanan, E.J. / Barr, K.J. / Zhu, J. / Paulvannan, K. / Yang, W. / Romanowski, M.J.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polo-like kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9372
Polymers34,4421
Non-polymers4941
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.129, 135.129, 135.129
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 Polo-like kinase 1


Mass: 34442.113 Da / Num. of mol.: 1 / Fragment: PLK1 kinase domain / Mutation: T196D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plk1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star Codon+ / References: UniProt: Q4KMI8, polo kinase
#2: Chemical ChemComp-FRS / 1-[5-methyl-2-(trifluoromethyl)furan-3-yl]-3-[(2Z)-5-(2-{[6-(1H-1,2,4-triazol-3-ylamino)pyrimidin-4-yl]amino}ethyl)-1,3-thiazol-2(3H)-ylidene]urea


Mass: 494.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17F3N10O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4, 22.5% PEG ...Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4, 22.5% PEG 3350, and 15% glycerol; cryoprotectant: 15% ethylene glycol., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2007
RadiationMonochromator: Side-scattering cube root I-beam bent single crystal; asymmetric cut 12.2 degs. Crystal type: Si(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 9717 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.2
Reflection shellResolution: 2.85→3 Å / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d5w

3d5w


Resolution: 2.85→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.607 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25722 1090 11.2 %RANDOM
Rwork0.22118 ---
obs0.22534 8622 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.325 Å2
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 34 16 2324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222364
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9953202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2555286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4623.039102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39115408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7131518
X-RAY DIFFRACTIONr_chiral_restr0.0590.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021792
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.21031
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21616
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5662.51473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.71852330
X-RAY DIFFRACTIONr_scbond_it1.152.51012
X-RAY DIFFRACTIONr_scangle_it1.9075872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.949 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.351 102 -
Rwork0.267 832 -
obs--100 %

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