[English] 日本語
Yorodumi
- PDB-9r1x: PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r1x
TitlePLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR BI 2536
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


positive regulation of mitotic nuclear envelope disassembly / 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 / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly ...positive regulation of mitotic nuclear envelope disassembly / 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 / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / Golgi inheritance / astral microtubule organization / mitotic cleavage furrow formation / outer kinetochore / microtubule bundle formation / mitotic chromosome condensation / double-strand break repair via alternative nonhomologous end joining / Polo-like kinase mediated events / regulation of mitotic spindle assembly / positive regulation of mitotic metaphase/anaphase transition / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / positive regulation of ubiquitin-dependent protein catabolic process / regulation of mitotic metaphase/anaphase transition / 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 / mitotic cytokinesis / mitotic sister chromatid segregation / 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 / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / 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 / centriole / 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 / kinetochore / positive regulation of protein localization to nucleus / G2/M transition of mitotic cell cycle / spindle / centriolar satellite / 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 / double-strand break repair / mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / regulation of cell cycle / 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 / cytoplasm / cytosol
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: 2.84 Å
AuthorsHillig, R.C. / Schulze, V.K. / Siemeister, G. / Schmitz, A.A. / Eberspaecher, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionApr 28, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,90112
Polymers73,0932
Non-polymers1,80810
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-87 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.515, 104.497, 71.329
Angle α, β, γ (deg.)90.00, 115.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-524-

HOH

-
Components

#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
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL GLY-SER ARE CLONING ARTIFACT FROM THROMBIN CLEAVAGE SITE. DOUBLE SURFACE ENTROPY REDUCTION (SER) MUTATION K225D/K226A DESIGNED TO INCREASE THE LIKELIHOOD OF CRYSTALLIZATION SUCCESS.
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
#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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 %
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: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.84→42.1 Å / Num. obs: 16036 / % possible obs: 91.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.3 Å2 / Rsym value: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 2.84→2.93 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1488 / Rsym value: 0.41 / % possible all: 53.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→42.1 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.856 / SU B: 42.54 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27746 817 5.1 %RANDOM
Rwork0.21875 ---
obs0.22166 15216 91.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.41 Å20 Å22.29 Å2
2---1.03 Å20 Å2
3----3.82 Å2
Refinement stepCycle: 1 / Resolution: 2.84→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 117 64 4904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135038
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154868
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.6736832
X-RAY DIFFRACTIONr_angle_other_deg1.0311.60911242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.520.325277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63315896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5721548
X-RAY DIFFRACTIONr_chiral_restr0.0390.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021172
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_it2.1383.3122363
X-RAY DIFFRACTIONr_mcbond_other2.1313.3112362
X-RAY DIFFRACTIONr_mcangle_it3.6457.4462958
X-RAY DIFFRACTIONr_mcangle_other3.6467.4482959
X-RAY DIFFRACTIONr_scbond_it2.2073.6052674
X-RAY DIFFRACTIONr_scbond_other2.1983.5922671
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7267.963857
X-RAY DIFFRACTIONr_long_range_B_refined6.5339.5235336
X-RAY DIFFRACTIONr_long_range_B_other6.52839.5335334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9324 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.842→2.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 28 -
Rwork0.306 580 -
obs--48.06 %
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)
14.7972-1.6881-0.47296.8831-0.93835.32250.0720.70090.49160.32820.1590.2559-0.9287-0.3353-0.2310.22950.0807-0.05760.18310.13370.332225.38514.859-1.76
22.9712-0.15920.43940.81930.09561.3301-0.02020.229-0.2294-0.08030.01920.12490.26960.01140.0010.0749-0.0109-0.03130.0195-0.01360.423235.626-4.91712.154
33.3194-1.2042-0.54334.1749-0.46424.4010.1522-0.1233-0.10640.6908-0.178-0.59720.29321.03420.02580.21310.0365-0.2010.37660.03960.568115.343-30.5134.641
42.36221.28010.01693.01640.03371.1706-0.05250.10790.30770.0020.00040.2344-0.13720.1220.05210.0305-0.0352-0.05140.04810.03240.5292-3.686-18.82820.782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 132
2X-RAY DIFFRACTION2A133 - 334
3X-RAY DIFFRACTION3B39 - 132
4X-RAY DIFFRACTION4B133 - 326

+
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