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- PDB-5nei: The structure of the polo-box domain (PBD) of polo-like kinase 1 ... -

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Basic information

Entry
Database: PDB / ID: 5nei
TitleThe structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with JES107
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / PLK1 / PBD1 / mitosis / small molecule
Function / homology
Function and homology information


positive regulation of mitotic nuclear envelope disassembly / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly ...positive regulation of mitotic nuclear envelope disassembly / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / astral microtubule organization / Golgi inheritance / outer kinetochore / mitotic cleavage furrow formation / microtubule bundle formation / mitotic chromosome condensation / double-strand break repair via alternative nonhomologous end joining / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-dependent protein catabolic process / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / regulation of mitotic cell cycle phase transition / mitotic spindle pole / spindle midzone / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic cytokinesis / mitotic sister chromatid segregation / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / Mitotic Prometaphase / regulation of mitotic cell cycle / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / establishment of protein localization / centriole / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / positive regulation of protein localization to nucleus / kinetochore / G2/M transition of mitotic cell cycle / spindle / centriolar satellite / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site ...POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / 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 / Alpha Beta
Similarity search - Domain/homology
Chem-8VB / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsKunciw, D.L. / Rossmann, M. / Stokes, J.E. / De Fusco, C. / Spring, D.R. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Sci Rep / Year: 2019
Title: A cryptic hydrophobic pocket in the polo-box domain of the polo-like kinase PLK1 regulates substrate recognition and mitotic chromosome segregation.
Authors: Sharma, P. / Mahen, R. / Rossmann, M. / Stokes, J.E. / Hardwick, B. / Huggins, D.J. / Emery, A. / Kunciw, D.L. / Hyvonen, M. / Spring, D.R. / McKenzie, G.J. / Venkitaraman, A.R.
History
DepositionMar 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 13, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8342
Polymers27,2851
Non-polymers5491
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.350, 91.360, 35.940
Angle α, β, γ (deg.)90.00, 99.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 27285.158 Da / Num. of mol.: 1 / Fragment: UNP residues Polo-box domain, 371-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53350, polo kinase
#2: Chemical ChemComp-8VB / 2-[[3-[[5-(3-iodanylphenyl)carbonylthiophen-2-yl]carbonylamino]phenyl]methyl]propanedioic acid / JES107 / polotyrin


Mass: 549.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16INO6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 10% PEG 3350, 100 mM Na/K tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.983 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2.68→91.36 Å / Num. obs: 5948 / % possible obs: 98.98 % / Redundancy: 2.6 % / Rsym value: 0.072 / Net I/σ(I): 9.56
Reflection shellResolution: 2.68→2.776 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.19 / Rsym value: 0.47 / % possible all: 99.37

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p2w

3p2w


Resolution: 2.68→45.68 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 269 4.52 %
Rwork0.1987 --
obs0.201 5947 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 31 11 1782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081832
X-RAY DIFFRACTIONf_angle_d1.1262488
X-RAY DIFFRACTIONf_dihedral_angle_d17.473681
X-RAY DIFFRACTIONf_chiral_restr0.068275
X-RAY DIFFRACTIONf_plane_restr0.008316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6802-3.37660.30261380.22882835X-RAY DIFFRACTION99
3.3766-45.68660.2241310.18732843X-RAY DIFFRACTION99

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