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- PDB-9im7: Crystal structure of mouse Plk1-PBD in complex with R12-4j compound -

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Basic information

Entry
Database: PDB / ID: 9im7
TitleCrystal structure of mouse Plk1-PBD in complex with R12-4j compound
Components
  • (ACE)(A1L2U)L(56A)S(YTH)(NH2)
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / PLK1 PBD / complex / inhibitor
Function / homology
Function and homology information


Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / Condensation of Prophase Chromosomes / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 ...Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / Condensation of Prophase Chromosomes / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein localization to organelle / regulation of protein localization to cell cortex / Resolution of Sister Chromatid Cohesion / The role of GTSE1 in G2/M progression after G2 checkpoint / synaptonemal complex disassembly / RHO GTPases Activate Formins / Separation of Sister Chromatids / polo kinase / homologous chromosome segregation / protein localization to nuclear envelope / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / female meiosis chromosome segregation / nuclear membrane disassembly / Regulation of PLK1 Activity at G2/M Transition / synaptonemal complex / anaphase-promoting complex binding / outer kinetochore / condensed chromosome, centromeric region / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic spindle assembly / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of double-strand break repair via homologous recombination / protein localization to chromatin / centriole / regulation of cytokinesis / spindle microtubule / establishment of protein localization / protein destabilization / kinetochore / centriolar satellite / G2/M transition of mitotic cell cycle / spindle / spindle pole / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / protein phosphorylation / protein kinase activity / 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 / ATP binding / identical protein binding / nucleus / 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 speciesMus musculus (house mouse)
synthetic constrcut (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKim, E.E. / Shin, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Pharmaceutics / Year: 2025
Title: N-Degron-Based PROTAC Targeting PLK1: A Potential Therapeutic Strategy for Cervical Cancer.
Authors: Gunasekaran, P. / Shin, S.C. / Hwang, Y.S. / Lee, J. / La, Y.K. / Yim, M.S. / Kim, H.N. / Kim, T.W. / Yang, E. / Lee, S.J. / Yoon, J.M. / Kim, E.E. / Jeon, S. / Ryu, E.K. / Bang, J.K.
History
DepositionJul 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: (ACE)(A1L2U)L(56A)S(YTH)(NH2)


Theoretical massNumber of molelcules
Total (without water)26,8162
Polymers26,8162
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.672, 51.454, 57.414
Angle α, β, γ (deg.)90.00, 100.90, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 25856.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plk1, Plk / Production host: Escherichia coli (E. coli) / References: UniProt: Q07832, polo kinase
#2: Protein/peptide (ACE)(A1L2U)L(56A)S(YTH)(NH2)


Mass: 959.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic constrcut (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.05 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: 0.1M Sodium malonate pH 5.4, 22% PEG3350

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 14849 / % possible obs: 97.6 % / Redundancy: 4.9 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.044 / Rrim(I) all: 0.107 / Χ2: 1.817 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.95-2.023.40.36614390.6670.8950.2090.4250.66495
2.02-2.13.60.31514560.8220.950.1740.3620.77796.2
2.1-2.24.40.27814590.8710.9650.140.3130.91498.1
2.2-2.314.60.23614970.930.9820.1140.2631.14397.8
2.31-2.464.70.19314680.9550.9880.0940.2161.12997.5
2.46-2.654.90.16414780.970.9920.0770.1821.33997.5
2.65-2.915.40.13414840.9820.9960.060.1471.73798.5
2.91-3.335.50.10815140.9880.9970.0490.1192.35398.3
3.33-4.26.20.08615150.9940.9980.0370.0943.08799
4.2-506.10.07215390.9950.9990.0310.0793.02797.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→38.01 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 1484 10 %
Rwork0.1787 --
obs0.1845 14835 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 68 69 1904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081871
X-RAY DIFFRACTIONf_angle_d1.332530
X-RAY DIFFRACTIONf_dihedral_angle_d11.543263
X-RAY DIFFRACTIONf_chiral_restr0.065280
X-RAY DIFFRACTIONf_plane_restr0.009316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.990.27221100.2177991X-RAY DIFFRACTION78
1.99-2.070.26831330.1951196X-RAY DIFFRACTION95
2.07-2.150.25771360.19151223X-RAY DIFFRACTION98
2.15-2.250.25781360.17411230X-RAY DIFFRACTION98
2.25-2.360.23931370.17841234X-RAY DIFFRACTION98
2.36-2.510.2441350.1861211X-RAY DIFFRACTION97
2.51-2.710.24641380.19241245X-RAY DIFFRACTION98
2.71-2.980.24231390.18931249X-RAY DIFFRACTION99
2.98-3.410.23861370.18181229X-RAY DIFFRACTION98
3.41-4.290.22541400.16431260X-RAY DIFFRACTION99
4.3-100.22221430.17191283X-RAY DIFFRACTION98

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