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- PDB-8wfp: Crystal structure of polo-like kinase(PLK1)PBD in complex with DD-1 -

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Basic information

Entry
Database: PDB / ID: 8wfp
TitleCrystal structure of polo-like kinase(PLK1)PBD in complex with DD-1
Components
  • DD-1
  • Serine/threonine-protein kinase PLK1
KeywordsSTRUCTURAL PROTEIN / Inhibitor
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 / regulation of mitotic spindle assembly / double-strand break repair via alternative nonhomologous end joining / 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 / positive regulation of proteolysis / mitotic cytokinesis / 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 / 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 / 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 / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / G2/M transition of mitotic cell cycle / 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-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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase 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. / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPark, J. / La, Y.K. / Bang, J.K. / Lee, S.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2022E0701018 Korea, Republic Of
CitationJournal: J.Med.Chem. / Year: 2024
Title: Degradation of Polo-like Kinase 1 by the Novel Poly-Arginine N-Degron Pathway PROTAC Regulates Tumor Growth in Nonsmall Cell Lung Cancer.
Authors: Gunasekaran, P. / Hwang, Y.S. / Lee, G.H. / Park, J. / Kim, J.G. / La, Y.K. / Park, N.Y. / Kothandaraman, R. / Yim, M.S. / Choi, J. / Kim, H.N. / Park, I.Y. / Lee, S.J. / Kim, M.H. / Cha- ...Authors: Gunasekaran, P. / Hwang, Y.S. / Lee, G.H. / Park, J. / Kim, J.G. / La, Y.K. / Park, N.Y. / Kothandaraman, R. / Yim, M.S. / Choi, J. / Kim, H.N. / Park, I.Y. / Lee, S.J. / Kim, M.H. / Cha-Molstad, H. / Shin, S.Y. / Ryu, E.K. / Bang, J.K.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Serine/threonine-protein kinase PLK1
C: DD-1
D: DD-1


Theoretical massNumber of molelcules
Total (without water)53,4234
Polymers53,4234
Non-polymers00
Water4,179232
1
A: Serine/threonine-protein kinase PLK1
C: DD-1


Theoretical massNumber of molelcules
Total (without water)26,7112
Polymers26,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area11180 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PLK1
D: DD-1


Theoretical massNumber of molelcules
Total (without water)26,7112
Polymers26,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-9 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.829, 35.370, 95.545
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number3
Space group name H-MP121

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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: 26052.740 Da / Num. of mol.: 2
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: Protein/peptide DD-1


Mass: 658.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5% PEG 3350, 10% Tacsimate pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→35.37 Å / Num. obs: 35270 / % possible obs: 96.56 % / Redundancy: 4 % / CC1/2: 0.995 / Net I/σ(I): 17.5
Reflection shellResolution: 1.99→4.79 Å / Num. unique obs: 35270 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9W

4o9w


Resolution: 1.99→35.37 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1987 5.63 %
Rwork0.1978 --
obs0.1995 35270 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 46 232 3961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d2.166
X-RAY DIFFRACTIONf_dihedral_angle_d14.643551
X-RAY DIFFRACTIONf_chiral_restr0.202569
X-RAY DIFFRACTIONf_plane_restr0.012653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.33951390.25912249X-RAY DIFFRACTION93
2.04-2.090.25541420.22092356X-RAY DIFFRACTION96
2.09-2.150.26191420.2122342X-RAY DIFFRACTION97
2.15-2.220.25491400.22112372X-RAY DIFFRACTION97
2.22-2.30.30521380.22352286X-RAY DIFFRACTION95
2.3-2.40.26291400.21792350X-RAY DIFFRACTION96
2.4-2.50.22521450.21162429X-RAY DIFFRACTION98
2.5-2.640.25671370.21232373X-RAY DIFFRACTION98
2.64-2.80.25231410.22682377X-RAY DIFFRACTION96
2.8-3.020.20891420.20892376X-RAY DIFFRACTION97
3.02-3.320.21751450.20422452X-RAY DIFFRACTION99
3.32-3.80.22221390.17972372X-RAY DIFFRACTION96
3.8-4.790.17491400.1632481X-RAY DIFFRACTION99
4.79-35.370.23711570.19762468X-RAY DIFFRACTION95

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