[English] 日本語
Yorodumi
- PDB-9r8b: CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r8b
TitleCRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN
Components
  • DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / DESIGN ANKYRIN REPEAT PROTEIN / DARPIN / SMALL MOLECULE INHIBITOR / DRUG DESIGN / KINASE / SERINE/THREONINE-PROTEIN KINASE / KINASE DOMAIN
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 / protein localization to nuclear envelope / Phosphorylation of Emi1 / homologous chromosome segregation ...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 / protein localization to nuclear envelope / Phosphorylation of Emi1 / homologous chromosome segregation / 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 / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / 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 / mitotic cytokinesis / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / positive regulation of proteolysis / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / negative regulation of double-strand break repair via homologous recombination / 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 / centriole / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Mitotic Prometaphase / Anchoring of the basal body to the plasma membrane / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / establishment of protein localization / RHO GTPases Activate Formins / peptidyl-serine phosphorylation / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / 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 / mitotic cell cycle / double-strand break repair / 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. / Matias, P.M. / Bandeiras, T.M. / Siemeister, G. / Schulze, V.K. / Schmitz, A.A. / Eberspaecher, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Polo-like kinase 1-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.,Sect.D / 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.
History
DepositionMay 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,8849
Polymers107,6184
Non-polymers1,2675
Water6,990388
1
A: Serine/threonine-protein kinase PLK1
C: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4254
Polymers53,8092
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-11 kcal/mol
Surface area19580 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PLK1
D: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4605
Polymers53,8092
Non-polymers6513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-19 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.072, 136.899, 140.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA37 - 3227 - 292
21ALAALAPROPROBB37 - 3227 - 292
12SERSERGLNGLNCC12 - 14212 - 142
22SERSERGLNGLNDD12 - 14212 - 142

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABCD

#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: N-Terminal GS IS CLONING ARTIFACT, FROM THROMBIN CLEAVAGE SITE SYNONYM: PLK-1, SERINE/THREONINE-PROTEIN KINASE 13, STPK13, POLO-LIKE KINASE 1, HUMAN POLO-LIKE KINASE 1;
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53350, polo kinase
#2: Protein DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10


Mass: 17835.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DESIGNED PROTEIN; VARIANT 3H10 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 393 molecules

#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 388 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
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 AT 303 K.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→68.54 Å / Num. obs: 56436 / % possible obs: 92.5 % / Redundancy: 2.9 % / Rrim(I) all: 0.059 / Net I/σ(I): 13.8
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 2.7 % / Num. unique obs: 8825 / Rrim(I) all: 0.886 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
PHASER1.3phasing
SCALAdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→68.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.123 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 2826 5 %RANDOM
Rwork0.18816 ---
obs0.19067 53613 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.325 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å2-0 Å2-0 Å2
2--1.36 Å2-0 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.2→68.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 85 388 7123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136960
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156771
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6559440
X-RAY DIFFRACTIONr_angle_other_deg1.3181.59615628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7235869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33721.699359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.799151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3871550
X-RAY DIFFRACTIONr_chiral_restr0.0810.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021529
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9223.1973401
X-RAY DIFFRACTIONr_mcbond_other4.9183.1953400
X-RAY DIFFRACTIONr_mcangle_it6.7397.154253
X-RAY DIFFRACTIONr_mcangle_other6.7397.1534254
X-RAY DIFFRACTIONr_scbond_it6.3013.6853559
X-RAY DIFFRACTIONr_scbond_other6.2963.6823557
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7647.9555173
X-RAY DIFFRACTIONr_long_range_B_refined10.92739.7757622
X-RAY DIFFRACTIONr_long_range_B_other10.92639.3447538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88490.13
12B88490.13
21C39010.11
22D39010.11
LS refinement shellResolution: 2.2→2.254 Å
RfactorNum. reflection% reflection
Rfree0.359 217 -
Rwork0.319 3536 -
obs--84.34 %
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)
12.94021.16721.37923.3099-0.82243.67520.06670.15780.1926-0.33670.01280.78140.2816-0.2292-0.07950.1909-0.0183-0.02220.0726-0.05890.2663-14.975-29.969-37.328
21.281-3.52950.95439.8018-2.82371.22420.1842-0.1241-0.318-0.58870.49221.03010.2554-0.4431-0.67640.2968-0.1603-0.07410.49460.25770.4801-3.762-23.636-41.966
31.51190.35030.20492.97450.44171.36350.1095-0.0194-0.23710.2696-0.1332-0.34720.1740.00970.02370.2357-0.04820.00020.0150.0140.0899.635-33.162-28.562
46.16250.36911.36533.14980.17551.16260.0287-0.09320.5040.37320.159-0.80320.06280.7226-0.18780.494-0.0228-0.13880.7641-0.22550.384530.8734.565-9.404
53.1609-2.12547.10081.4486-5.03919.7338-0.10640.40430.59520.1012-0.2872-0.3446-0.42741.22790.39350.3136-0.0818-0.09840.3454-0.13280.487617.2366.467-11.412
61.40110.7222-0.43490.86620.48363.01110.1037-0.2388-0.02660.66780.0678-0.16591.05310.5986-0.17150.99540.1215-0.17810.2271-0.05420.056810.811-11.346-2.441
73.106-0.2632-0.59174.52630.4162.7537-0.04490.41590.1352-0.7819-0.0488-0.1824-0.18930.18460.09370.4512-0.00620.0610.12420.05380.03439.319-8.673-50.664
81.9942-0.3894-0.13652.6485-0.51744.54890.0014-0.14480.24410.26210.02480.2269-0.6678-0.2107-0.02620.4538-0.00010.01590.0245-0.02540.1748-1.81213.798-19.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 132
2X-RAY DIFFRACTION2A1001
3X-RAY DIFFRACTION3A133 - 326
4X-RAY DIFFRACTION4B37 - 132
5X-RAY DIFFRACTION5B402
6X-RAY DIFFRACTION6B133 - 323
7X-RAY DIFFRACTION7C12 - 145
8X-RAY DIFFRACTION8D12 - 143

+
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