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- PDB-9r8c: CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH... -

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Entry
Database: PDB / ID: 9r8c
TitleCRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN
Components
  • DESIGNED ANKYRIN REPEAT PROTEIN 3H10
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / DESIGN ANKYRIN REPEAT PROTEIN / DARPIN / SMALL MOLECULE INHIBITOR / DRUG DESIGN / KINASE / SERINE/THREONINE-PROTEIN 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 / 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 / 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 / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Mitotic Prometaphase / centriole / Recruitment of mitotic centrosome proteins and complexes / EML4 and NUDC in mitotic spindle formation / 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 / mitotic spindle organization / regulation of cytokinesis / 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 / peptidyl-serine phosphorylation / protein destabilization / kinetochore / positive regulation of protein localization to nucleus / G2/M transition of mitotic cell cycle / centriolar satellite / 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 / 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
Chem-R78 / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.243 Å
AuthorsHillig, R.C. / Matias, P.M. / Bandeiras, T.M. / Schulze, V.K. / Siemeister, G. / Schmitz, A.A. / Eberspaecher, U. / Bomer, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2025
Title: PLK1-Inhibitor Co-complex Structures via the Surface Entropy Reduction Approach and a DARPin-assisted Approach
Authors: Eberspaecher, U. / Schmitz, A.A. / Siemeister, G. / Bomer, U. / Bandeiras, T.M. / Matias, P.M. / Schulze, V.K. / Hillig, R.C.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2008
Title: Structure of wild-type Plk-1 kinase domain in complex with a selective DARPin.
Authors: Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghanel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Putter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / ...Authors: Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghanel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Putter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / Holz, C. / Schmitz, A.A. / Lang, C. / Donner, P. / Egner, U. / Carrondo, M.A. / Muller-Tiemann, B. / Eberspaecher, U. / Bomer, U.
History
DepositionMay 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Serine/threonine-protein kinase PLK1
C: DESIGNED ANKYRIN REPEAT PROTEIN 3H10
D: DESIGNED ANKYRIN REPEAT PROTEIN 3H10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,02910
Polymers107,6184
Non-polymers1,4126
Water5,927329
1
A: Serine/threonine-protein kinase PLK1
D: DESIGNED ANKYRIN REPEAT PROTEIN 3H10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6076
Polymers53,8092
Non-polymers7984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-8 kcal/mol
Surface area19350 Å2
2
B: Serine/threonine-protein kinase PLK1
C: DESIGNED ANKYRIN REPEAT PROTEIN 3H10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4234
Polymers53,8092
Non-polymers6142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-7 kcal/mol
Surface area19400 Å2
Unit cell
Length a, b, c (Å)62.605, 135.302, 136.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSPROPROAA38 - 3228 - 292
211LYSLYSPROPROAA38 - 3228 - 292
322GLUGLULYSLYSB - AB - A42 - 14312 - 113
422GLUGLULYSLYSB - AB - A42 - 14312 - 113

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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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: 35972.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SYNONYM: PLK-1, SERINE/THREONINE-PROTEIN KINASE 13, STPK13, POLO-LIKE KINASE 1, HUMAN POLO-LIKE KINASE 1; N-TERMINAL GLY-SER ARE CLONING ARTIFACT FROM THROMBIN CLEAVAGE SITE.
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Spodoptera frugiperda ascovirus 1a / References: UniProt: P53350, polo kinase
#2: Protein DESIGNED ANKYRIN REPEAT PROTEIN 3H10


Mass: 17835.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal HIS Affinity Tag / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.037 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.24→96.16 Å / Num. obs: 233157 / % possible obs: 97.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 40.5 Å2 / Rrim(I) all: 0.084 / Net I/σ(I): 14.6
Reflection shellResolution: 2.24→2.38 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 28100 / Rrim(I) all: 1.118 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
SCALAdata scaling
PHASER1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.243→48.128 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.941 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.236 2826 5.106 %
Rwork0.1882 52521 -
all0.191 --
obs-55347 98.06 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.407 Å2
Baniso -1Baniso -2Baniso -3
1-0.604 Å20 Å2-0 Å2
2---0.436 Å20 Å2
3----0.168 Å2
Refinement stepCycle: LAST / Resolution: 2.243→48.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 100 329 7049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0126927
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166740
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.8699385
X-RAY DIFFRACTIONr_angle_other_deg0.5051.78715556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.415855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.278550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.776101219
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.08810310
X-RAY DIFFRACTIONr_chiral_restr0.0690.21061
X-RAY DIFFRACTIONr_chiral_restr_other0.0320.228
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
X-RAY DIFFRACTIONr_nbd_refined0.2150.21388
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26223
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23361
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2291
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.210
X-RAY DIFFRACTIONr_nbd_other0.1850.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.29
X-RAY DIFFRACTIONr_mcbond_it4.8762.8253375
X-RAY DIFFRACTIONr_mcbond_other4.8762.8253375
X-RAY DIFFRACTIONr_mcangle_it6.7967.5894218
X-RAY DIFFRACTIONr_mcangle_other6.8027.594219
X-RAY DIFFRACTIONr_scbond_it6.0443.3273552
X-RAY DIFFRACTIONr_scbond_other6.0443.3293553
X-RAY DIFFRACTIONr_scangle_it8.4718.7595158
X-RAY DIFFRACTIONr_scangle_other8.478.7615159
X-RAY DIFFRACTIONr_lrange_it10.33230.6437633
X-RAY DIFFRACTIONr_lrange_other10.33930.47586
X-RAY DIFFRACTIONr_ncsr_local_group_10.1250.059080
X-RAY DIFFRACTIONr_ncsr_local_group_20.0930.054117
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.125320.05008
12AX-RAY DIFFRACTIONLocal ncs0.125320.05008
23AX-RAY DIFFRACTIONLocal ncs0.092550.0501
24AX-RAY DIFFRACTIONLocal ncs0.092550.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.243-2.3010.3681950.3431710.34240720.90.91482.66210.324
2.301-2.3640.3251990.31637740.31640020.9250.93299.27540.286
2.364-2.4320.2711930.26537040.26539020.9580.95899.87190.234
2.432-2.5070.3482140.24335970.24838130.9370.96599.94750.205
2.507-2.5890.31860.2434750.24336630.9410.96599.94540.2
2.589-2.680.2781850.2133620.21435480.9610.97399.97180.169
2.68-2.780.2691750.19232720.19634480.9590.97899.9710.15
2.78-2.8940.2241620.17731640.17933310.9710.98199.84990.142
2.894-3.0220.2211730.1730090.17231910.9690.98399.7180.141
3.022-3.1690.2381530.18428820.18630470.9680.9899.60620.158
3.169-3.3390.2571350.19927600.20229050.9610.97899.65580.179
3.339-3.5410.2491330.19326130.19627680.9740.98399.20520.179
3.541-3.7840.2241390.18624400.18826010.9690.98599.15420.175
3.784-4.0850.2241220.16822670.17124280.9740.98698.39370.158
4.085-4.4710.1571070.13321270.13522720.9850.9998.32750.129
4.471-4.9940.1741010.13819100.13920380.9830.9998.67520.135
4.994-5.7560.238860.17617200.17918360.9690.98598.3660.169
5.756-7.0240.282740.18514550.18915610.9610.98397.950.18
7.024-9.830.184570.15611540.15712390.9780.98697.74010.169
9.83-48.1280.242370.2346650.2347690.9660.9691.28740.266
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7538-0.7255-2.52.1476-0.86124.52940.0379-0.12020.13980.23880.17180.8007-0.4355-0.4395-0.20970.31120.04540.03790.21510.00920.3928-15.612630.763634.0172
21.7844-0.03920.10573.0087-0.23871.9421-0.017-0.02480.1155-0.1620.0122-0.2463-0.04210.11950.00480.2080.05390.01850.0734-0.01050.029110.141531.921729.046
32.40480.889-3.20638.8459-9.303212.0129-0.0206-0.2887-0.03280.58970.09490.1059-0.54120.2008-0.07440.2454-0.0008-0.00980.2256-0.01150.1239-5.690824.954640.4608
43.2638-0.9305-1.34243.62750.3442.2444-0.0045-0.2087-0.23410.09630.0367-0.62820.18330.6671-0.03220.2880.0717-0.01280.3385-0.02850.173231.8914-2.599710.4279
51.83910.30120.08342.2524-0.56222.3391-0.10430.0947-0.0503-0.19180.17230.0112-0.1933-0.0943-0.0680.32040.05940.0530.1046-0.00030.012811.455611.77892.0578
610.411111.93972.634917.49941.77741.2087-0.30330.4439-0.1677-0.60620.49050.07970.17940.0667-0.18720.31640.0279-0.05190.21620.0130.159519.037-5.87279.8789
73.10130.48620.11562.91530.98143.5850.06120.3107-0.1868-0.1678-0.06020.21610.0707-0.3039-0.00090.23270.03090.00220.08420.01010.0751-2.0117-13.995617.5954
81.5646-0.14070.62162.77240.77323.65560.0272-0.1836-0.08420.22250.0398-0.06640.13360.0328-0.06690.24110.05140.0170.10970.03450.01475.90337.243450.2625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA39 - 131
2X-RAY DIFFRACTION2ALLA132 - 326
3X-RAY DIFFRACTION3ALLA1001

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