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- PDB-5nmm: The structure of the polo-box domain (PBD) of Plk1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5nmm
TitleThe structure of the polo-box domain (PBD) of Plk1 in complex with Alpha-Bromo-3-Iodotoluene.
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / PLK1 / PBD1 / mitosis / small molecule
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / protein localization to nuclear envelope / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic spindle assembly / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / mitotic cytokinesis / positive regulation of proteolysis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / protein localization to chromatin / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / peptidyl-serine phosphorylation / microtubule binding / regulation of cell cycle / protein kinase activity / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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 / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / 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 / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / 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
Alpha-Bromo-3-Iodotoluene / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 Å
AuthorsKunciw, D.L. / Rossmann, M. / Stokes, J.E. / De Fusco, C. / Spring, D.R. / Hyvonen, M.
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
DepositionApr 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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)27,5822
Polymers27,2851
Non-polymers2971
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.360, 93.040, 35.910
Angle α, β, γ (deg.)90.00, 100.22, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase
#2: Chemical ChemComp-8Z5 / Alpha-Bromo-3-Iodotoluene


Mass: 296.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6BrI
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 200 mM K/Na Tartrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.02→46.52 Å / Num. obs: 13900 / % possible obs: 98.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.044 / Net I/σ(I): 11.4
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1009 / Rpim(I) all: 0.618 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2.02→46.52 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.93
RfactorNum. reflection% reflection
Rfree0.237 730 5.26 %
Rwork0.1924 --
obs0.1948 13878 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 9 34 1763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051765
X-RAY DIFFRACTIONf_angle_d0.8682390
X-RAY DIFFRACTIONf_dihedral_angle_d12.189642
X-RAY DIFFRACTIONf_chiral_restr0.048268
X-RAY DIFFRACTIONf_plane_restr0.003301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0201-2.17610.32761420.25882597X-RAY DIFFRACTION97
2.1761-2.3950.29551610.23092634X-RAY DIFFRACTION98
2.395-2.74160.25071490.20792618X-RAY DIFFRACTION99
2.7416-3.45390.2441140.19782679X-RAY DIFFRACTION99
3.4539-46.53230.21061640.17072620X-RAY DIFFRACTION97

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