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- PDB-4whl: A New Class of Peptidomimetics Targeting the Polo-box Domain of P... -

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Basic information

Entry
Database: PDB / ID: 4whl
TitleA New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1
Components
  • C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Polo-like kinase / Polo-box domain / Inhibitor / peptide derivative / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / regulation of protein binding / 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 / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / centriolar satellite / mitotic cytokinesis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / 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 / microtubule binding / peptidyl-serine phosphorylation / 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 / 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 / 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
C6H5(CH2)8-derivatized peptide inhibitor / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsBang, J.K. / Han, Y.H. / Ahn, M.J. / Lee, K.S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Korea Basic Science InstituteT34418 Korea, Republic Of
Rural Development AdministrationPJ009594 Korea, Republic Of
CitationJournal: J.Med.Chem. / Year: 2015
Title: A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1.
Authors: Ahn, M. / Han, Y.H. / Park, J.E. / Kim, S. / Lee, W.C. / Lee, S.J. / Gunasekaran, P. / Cheong, C. / Shin, S.Y. / Kim, H.Y. / Ryu, E.K. / Murugan, R.N. / Kim, N.H. / Bang, J.K.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Structure summary
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)28,0842
Polymers28,0842
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.760, 57.760, 137.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 371-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53350, polo kinase
#2: Protein/peptide C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR


Type: Polypeptide / Class: Enzyme inhibitor / Mass: 798.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: C6H5(CH2)8-derivatized peptide inhibitor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1M Citric acid, 28% PEG8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 6904 / % possible obs: 99.9 % / Redundancy: 16.4 % / Net I/σ(I): 8.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
ADSCdata collection
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2308 / WRfactor Rwork: 0.1639 / FOM work R set: 0.8266 / SU B: 11.797 / SU ML: 0.246 / SU Rfree: 0.3533 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 340 5 %RANDOM
Rwork0.1822 6519 --
obs0.1854 6519 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.13 Å2 / Biso mean: 47.345 Å2 / Biso min: 26.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å20 Å2
2---1.69 Å20 Å2
3---3.39 Å2
Refinement stepCycle: final / Resolution: 2.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 56 1 1832
Biso mean--40.8 34.79 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021819
X-RAY DIFFRACTIONr_bond_other_d0.0040.021696
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9922463
X-RAY DIFFRACTIONr_angle_other_deg1.0753.0113897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9175214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62523.46278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.92315305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8091512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02427
X-RAY DIFFRACTIONr_mcbond_it3.4534.682865
X-RAY DIFFRACTIONr_mcbond_other3.4554.684863
X-RAY DIFFRACTIONr_mcangle_it5.4567.0061076
LS refinement shellResolution: 2.706→2.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 34 -
Rwork0.221 464 -
all-498 -
obs--100 %

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