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- PDB-4e67: The structure of the polo-box domain (PBD) of polo-like kinase 1 ... -

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Basic information

Entry
Database: PDB / ID: 4.0E+67
TitleThe structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with hydrocinnamoyl-derivatized PLHSpTA peptide
Components
  • Serine/threonine-protein kinase PLK1
  • hydrocinnamoyl-derivatized PLHSpTA peptide
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Serine/threonine-protein kinase / TRANSFERASE / Phosphoprotein-binding domain / 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 / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope / Phosphorylation of Emi1 / nuclear membrane disassembly / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / anaphase-promoting complex binding / outer kinetochore / positive regulation of ubiquitin protein ligase activity / double-strand break repair via alternative nonhomologous end joining / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / positive regulation of ubiquitin-protein transferase activity / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic cytokinesis / mitotic sister chromatid segregation / spindle midzone / 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 / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / regulation of cytokinesis / mitotic spindle organization / RHO GTPases Activate Formins / establishment of protein localization / 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 / centriolar satellite / spindle / spindle pole / G2/M transition of mitotic cell cycle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / microtubule binding / protein kinase activity / regulation of cell cycle / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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 / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / 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 / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / 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
hydrocinnamoyl-derivatized PLHSpTA peptide / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSledz, P. / Hyvonen, M. / Tan, Y.S. / Lang, S. / Spring, D. / Abell, C. / Best, R.B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1.
Authors: Tan, Y.S. / Sledz, P. / Lang, S. / Stubbs, C.J. / Spring, D.R. / Abell, C. / Best, R.B.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 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: hydrocinnamoyl-derivatized PLHSpTA peptide


Theoretical massNumber of molelcules
Total (without water)27,5912
Polymers27,5912
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.492, 50.906, 57.910
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211

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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: 26755.518 Da / Num. of mol.: 1 / Fragment: Polo box domain (PBD), residues 371-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase
#2: Protein/peptide hydrocinnamoyl-derivatized PLHSpTA peptide


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 835.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid-state peptide synthesis / References: hydrocinnamoyl-derivatized PLHSpTA peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.86 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 0.1 M sodium azide and 22% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5406 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 15, 2011
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→56.84 Å / Num. all: 11989 / Num. obs: 11821 / % possible obs: 98.6 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.2 Å / % possible all: 90.6

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p2z

3p2z


Resolution: 2.1→56.84 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.669 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26494 562 4.8 %RANDOM
Rwork0.21569 ---
obs0.21801 11235 98.54 %-
all-11989 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.274 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 0 76 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221815
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.9712463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3555221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56222.68382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61415307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7551515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211361
X-RAY DIFFRACTIONr_mcbond_it0.3581.51103
X-RAY DIFFRACTIONr_mcangle_it0.69221777
X-RAY DIFFRACTIONr_scbond_it0.9413712
X-RAY DIFFRACTIONr_scangle_it1.534.5684
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 37 -
Rwork0.255 700 -
obs--84.81 %

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