[English] 日本語
Yorodumi
- PDB-9r1w: PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH THIAZ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r1w
TitlePLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / SURFACE ENTROPY REDUCTION / SER / 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
: / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHillig, R.C. / Schulze, V.K. / Siemeister, G. / Schmitz, A.A. / Eberspaecher, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallographica Section 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.
History
DepositionApr 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Serine/threonine-protein kinase PLK1
BBB: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,21216
Polymers73,0932
Non-polymers2,11914
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The PLK1 kinase domain is assumed to be a monomer in solution. The dimer is most likely a crystallization artifact.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-86 kcal/mol
Surface area28460 Å2
Unit cell
Length a, b, c (Å)113.048, 103.921, 70.799
Angle α, β, γ (deg.)90.000, 115.435, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11BBB-158-

ARG

21AAA-590-

HOH

31BBB-503-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 38 - 324 / Label seq-ID: 23 - 309

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 36546.387 Da / Num. of mol.: 2 / Mutation: K225D, K226A
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL GLY-SER ARE CLONING ARTIFACT FROM THROMBIN CLEAVAGE SITE. DOUBLE MUTATION K225D, K226A INTRODUCED AS SURFACE ENTROPY REDUCTION MUTATION TO INCREASE THE LIKELIHOOD TO OBTAIN CRYSTALS.
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53350, polo kinase

-
Non-polymers , 5 types, 199 molecules

#2: Chemical ChemComp-A1JCP / (2~{Z})-2-cyano-2-[3-ethyl-5-[(~{E})-[2-[methyl-(1-methylpiperidin-4-yl)amino]pyridin-4-yl]iminomethyl]-4-oxidanylidene-1,3-thiazol-2-ylidene]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide


Mass: 523.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28F3N7O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.4 % / Description: arrow-head shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: sodium acetate, ammonium sulphate, MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9537 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→36.9 Å / Num. obs: 32885 / % possible obs: 87.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.4 Å2 / Rsym value: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5102 / Rsym value: 0.42 / % possible all: 52.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.989 / SU ML: 0.163 / SU R Cruickshank DPI: 0.1694 / Cross valid method: FREE R-VALUE / ESU R: 0.292 / ESU R Free: 0.205 / SU Rfree Cruickshank DPI: 0.2056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 1641 4.991 %Random selection
Rwork0.1779 31239 --
all0.18 ---
obs-31239 87.266 %-
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: 61.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.245 Å2-0 Å21.24 Å2
2---0.692 Å20 Å2
3---0.521 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 133 185 5053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154946
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.6716949
X-RAY DIFFRACTIONr_angle_other_deg1.1221.60111441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37720.493284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40715920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1691549
X-RAY DIFFRACTIONr_chiral_restr0.0550.2647
X-RAY DIFFRACTIONr_chiral_restr_other0.0220.220
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021186
X-RAY DIFFRACTIONr_nbd_refined0.1880.2919
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.24389
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22415
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2211
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.216
X-RAY DIFFRACTIONr_nbd_other0.2010.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_mcbond_it2.8553.4462392
X-RAY DIFFRACTIONr_mcbond_other2.8513.4442391
X-RAY DIFFRACTIONr_mcangle_it4.5837.7353000
X-RAY DIFFRACTIONr_mcangle_other4.5837.7393001
X-RAY DIFFRACTIONr_scbond_it3.8864.052725
X-RAY DIFFRACTIONr_scbond_other3.8854.0522726
X-RAY DIFFRACTIONr_scangle_it6.1088.8473927
X-RAY DIFFRACTIONr_scangle_other6.1078.853928
X-RAY DIFFRACTIONr_lrange_it8.48942.3755531
X-RAY DIFFRACTIONr_lrange_other8.50642.2595506
X-RAY DIFFRACTIONr_ncsr_local_group_10.0850.059391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.084580.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.084580.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.316710.261222X-RAY DIFFRACTION46.797
2.254-2.3160.274660.2451543X-RAY DIFFRACTION59.6368
2.316-2.3830.234920.2271666X-RAY DIFFRACTION66.9969
2.383-2.4560.254950.2161858X-RAY DIFFRACTION75.9627
2.456-2.5360.2591070.2051958X-RAY DIFFRACTION83.0652
2.536-2.6250.292990.2042105X-RAY DIFFRACTION91.8333
2.625-2.7240.2561170.2032126X-RAY DIFFRACTION97.3524
2.724-2.8350.2391080.1852116X-RAY DIFFRACTION99.5524
2.835-2.9610.2181120.1852018X-RAY DIFFRACTION99.9062
2.961-3.1060.285950.1971921X-RAY DIFFRACTION100
3.106-3.2730.2421130.1881836X-RAY DIFFRACTION99.8463
3.273-3.4710.194800.1751779X-RAY DIFFRACTION99.7853
3.471-3.710.232970.1771612X-RAY DIFFRACTION99.4761
3.71-4.0070.158720.141544X-RAY DIFFRACTION99.5687
4.007-4.3880.152730.1291406X-RAY DIFFRACTION99.7303
4.388-4.9040.179790.1411260X-RAY DIFFRACTION99.3323
4.904-5.6580.216590.181131X-RAY DIFFRACTION99.4983
5.658-6.9190.243490.207968X-RAY DIFFRACTION99.8037
6.919-9.7410.156360.162750X-RAY DIFFRACTION99.4937
9.741-36.90.231210.2420X-RAY DIFFRACTION96.2882
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)
15.2294-0.2478-0.31255.5829-0.31433.941-0.02440.89670.7413-0.14040.22630.4305-0.8052-0.5702-0.20190.45080.08360.03980.29630.2170.192325.65214.77-1.657
23.20540.09840.55241.54490.04961.56030.00560.1884-0.3013-0.1498-0.00250.04220.25860.0286-0.00310.1898-0.02850.0820.018-0.03430.088735.943-4.92412.009
36.92510.99030.96985.05781.31766.42680.3755-0.051-0.53410.5060.0822-1.2110.8921.6887-0.45770.30410.1757-0.11890.5847-0.01260.489915.074-30.44534.789
42.56561.5589-0.34123.09650.0231.1165-00.07250.4993-0.0790.07780.2754-0.12280.0933-0.07780.1497-0.04960.05630.03580.0480.3094-3.485-18.64820.549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA38 - 132
2X-RAY DIFFRACTION2ALLAAA133 - 334
3X-RAY DIFFRACTION3ALLBBB38 - 132
4X-RAY DIFFRACTION4ALLBBB133 - 325

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more