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- PDB-4whk: A New Class of Peptidomimetics Targeting the Polo-box Domain of P... -

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Basic information

Entry
Database: PDB / ID: 4whk
TitleA New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1
Components
  • C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Polo-like kinase / Inhibitor / peptide derivative / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / positive regulation of ubiquitin-protein transferase activity / 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 / 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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / 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 / 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 / protein destabilization / peptidyl-serine phosphorylation / kinetochore / positive regulation of protein localization to nucleus / centriolar satellite / G2/M transition of mitotic cell cycle / 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 / cytoplasm / cytosol
Similarity search - Function
POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site ...POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / Arylsulfatase, C-terminal domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
C6H5(CH2)8-derivatized peptide inhibitor / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBang, J.K. / Han, Y.H. / Ahn, M.J. / Lee, K.S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Korea Basic Science InstituteT34418 Korea, Republic Of
Rural Development AdministrationPJ009594 Korea, Republic Of
CitationJournal: J.Med.Chem. / Year: 2015
Title: A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1.
Authors: Ahn, M. / Han, Y.H. / Park, J.E. / Kim, S. / Lee, W.C. / Lee, S.J. / Gunasekaran, P. / Cheong, C. / Shin, S.Y. / Kim, H.Y. / Ryu, E.K. / Murugan, R.N. / Kim, N.H. / Bang, J.K.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)28,0812
Polymers28,0812
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-7 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.592, 39.651, 39.942
Angle α, β, γ (deg.)93.730, 97.090, 102.920
Int Tables number1
Space group name H-MP1

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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: 27285.158 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 371-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53350, polo kinase
#2: Protein/peptide C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR


Type: Polypeptide / Class: Enzyme inhibitor / Mass: 795.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: C6H5(CH2)8-derivatized peptide inhibitor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4M K-Na tartrate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20085 / % possible obs: 97.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.035 / Χ2: 2.093 / Net I/av σ(I): 33.3 / Net I/σ(I): 20.6 / Num. measured all: 47511
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.832.40.1299872.0196
1.83-1.862.40.11981296.3
1.86-1.92.40.10310042.1696.1
1.9-1.942.40.0939872.13396.2
1.94-1.982.40.08710182.83196.3
1.98-2.032.40.0749802.52397
2.03-2.082.40.07110262.42696.3
2.08-2.132.40.0629702.39297.2
2.13-2.22.40.05510112.3296.8
2.2-2.272.40.0549892.62897.2
2.27-2.352.40.05310562.38997.6
2.35-2.442.40.0489752.27497.1
2.44-2.552.40.04610152.298.2
2.55-2.692.40.03910292.04198
2.69-2.862.40.03610131.90698
2.86-3.082.30.03210241.82198.3
3.08-3.392.40.02610081.49798.5
3.39-3.882.30.02310071.37898.5
3.88-4.882.30.02110191.19597.6
4.88-502.30.0259861.64195.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
ADSC2.5.1data collection
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HIH

3hih


Resolution: 1.8→39.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2091 / WRfactor Rwork: 0.1681 / FOM work R set: 0.882 / SU B: 2.235 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1213 / SU Rfree: 0.1155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 1026 5.1 %RANDOM
Rwork0.1591 19059 --
obs0.161 20085 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.84 Å2 / Biso mean: 20.392 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20.97 Å2-1.9 Å2
2---0.46 Å2-0.58 Å2
3----1.31 Å2
Refinement stepCycle: final / Resolution: 1.8→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 1 100 1924
Biso mean--18.59 26.68 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191869
X-RAY DIFFRACTIONr_bond_other_d0.0020.021760
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9922525
X-RAY DIFFRACTIONr_angle_other_deg1.4133.0064053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.55523.61483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87615326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5731512
X-RAY DIFFRACTIONr_chiral_restr0.1330.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022061
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02438
X-RAY DIFFRACTIONr_mcbond_it1.8411.826889
X-RAY DIFFRACTIONr_mcbond_other1.8411.826888
X-RAY DIFFRACTIONr_mcangle_it2.6272.731106
LS refinement shellResolution: 1.792→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 72 -
Rwork0.196 1226 -
all-1298 -
obs--84.84 %

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