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- PDB-3p2z: Polo-like kinase I Polo-box domain in complex with PLHSpTA phosph... -

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Basic information

Entry
Database: PDB / ID: 3p2z
TitlePolo-like kinase I Polo-box domain in complex with PLHSpTA phosphopeptide from PBIP1
Components
  • Serine/threonine-protein kinase PLK1
  • phosphopeptide
KeywordsTRANSFERASE / phosphoprotein binding domain / Plk1 / KINASE
Function / homology
Function and homology information


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 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / Phosphorylation of Emi1 ...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 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / nuclear membrane disassembly / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / Golgi inheritance / outer kinetochore / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of mitotic spindle assembly / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / mitotic cytokinesis / positive regulation of proteolysis / 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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / 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 / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / regulation of cytokinesis / mitotic spindle organization / establishment of protein localization / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / peptidyl-serine phosphorylation / kinetochore / positive regulation of protein localization to nucleus / centriolar satellite / G2/M transition of mitotic cell cycle / spindle / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / regulation of cell cycle / protein ubiquitination / 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
Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSledz, P. / Stubbs, C.J. / Hyvonen, M. / Abell, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: From crystal packing to molecular recognition: prediction and discovery of a binding site on the surface of polo-like kinase 1
Authors: Sledz, P. / Stubbs, C.J. / Lang, S. / Yang, Y.Q. / McKenzie, G.J. / Venkitaraman, A.R. / Hyvonen, M. / Abell, C.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,5773
Polymers27,4852
Non-polymers921
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.412, 66.863, 43.427
Angle α, β, γ (deg.)90.00, 94.12, 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: 26755.518 Da / Num. of mol.: 1 / Fragment: Polo-box domain
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 (E. coli) / References: UniProt: P53350, polo kinase
#2: Protein/peptide phosphopeptide


Mass: 729.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M K/Na tartrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorDate: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.79→43.31 Å / Num. obs: 18437 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UMW (chain A)

1umw


Resolution: 1.79→43.31 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.096 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24974 945 5.1 %RANDOM
Rwork0.20252 ---
all0.20482 ---
obs0.20252 17491 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.961 Å2
Refinement stepCycle: LAST / Resolution: 1.79→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 6 146 1887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221809
X-RAY DIFFRACTIONr_angle_refined_deg0.9331.972459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0955222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.94222.8481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1815301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5281513
X-RAY DIFFRACTIONr_chiral_restr0.0610.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211345
X-RAY DIFFRACTIONr_mcbond_it0.3331.51095
X-RAY DIFFRACTIONr_mcangle_it0.64621765
X-RAY DIFFRACTIONr_scbond_it0.8543714
X-RAY DIFFRACTIONr_scangle_it1.4514.5689
LS refinement shellResolution: 1.791→1.838 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 52 -
Rwork0.308 1254 -
obs--97.24 %
Refinement TLS params.Method: refined / Origin x: 15.532 Å / Origin y: 1.996 Å / Origin z: 10.508 Å
111213212223313233
T0.0506 Å20.0182 Å2-0.0583 Å2-0.0451 Å2-0.0115 Å2--0.0771 Å2
L1.0944 °20.4029 °2-0.9226 °2-1.1642 °2-0.7526 °2--2.3482 °2
S-0.0539 Å °-0.0455 Å °-0.0096 Å °-0.0391 Å °0.0219 Å °0.0074 Å °0.083 Å °0.0741 Å °0.032 Å °

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