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- PDB-4o6w: Peptide-Based Inhibitors of Plk1 Polo-box Domain -

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Basic information

Entry
Database: PDB / ID: 4o6w
TitlePeptide-Based Inhibitors of Plk1 Polo-box Domain
Components
  • Peptide-Based inhibitor
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Polo box domain / phospho-peptide binding / phosphopeptide / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / regulation of protein binding / anaphase-promoting complex binding / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / mitotic chromosome condensation / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic cytokinesis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / kinetochore / spindle pole / spindle / positive regulation of protein localization to nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / peptidyl-serine phosphorylation / protein ubiquitination / regulation of cell cycle / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / 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
Phosphothreonine ester-containing peptide / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.448 Å
AuthorsQian, W.-J. / Park, J.-E. / Lim, D.C. / Park, S.-Y. / Lee, K.-W. / Yaffe, M.B. / Lee, K.S. / Burke, T.R.
CitationJournal: Biopolymers / Year: 2014
Title: Mono-anionic phosphopeptides produced by unexpected histidine alkylation exhibit high plk1 polo-box domain-binding affinities and enhanced antiproliferative effects in hela cells.
Authors: Qian, W.J. / Park, J.E. / Lim, D. / Lai, C.C. / Kelley, J.A. / Park, S.Y. / Lee, K.W. / Yaffe, M.B. / Lee, K.S. / Burke, T.R.
History
DepositionDec 23, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionDec 3, 2014ID: 4MLU
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
C: Peptide-Based inhibitor


Theoretical massNumber of molelcules
Total (without water)28,2202
Polymers28,2202
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-9 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.819, 51.275, 58.006
Angle α, β, γ (deg.)90.00, 101.19, 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: 27285.158 Da / Num. of mol.: 1 / Fragment: Polo box domain (UNP residues 371-603)
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 Peptide-Based inhibitor


Type: PolypeptidePeptide / Class: Enzyme inhibitor / Mass: 935.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Phosphothreonine ester-containing peptide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 1.85 Å3/Da / Density % sol: 33.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13% (w/v) PEG 3350, 0.1 M HEPES pH 7.5 and 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 20, 2012 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→15 Å / Num. all: 35368 / Num. obs: 35356 / % possible obs: 99.97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3413 / Rsym value: 0.225 / % possible all: 94.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.448→14.86 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 2000 5.66 %RANDOM
Rwork0.1837 ---
obs0.1854 35356 96.08 %-
all-35368 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.448→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 0 218 2053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031968
X-RAY DIFFRACTIONf_angle_d0.8442658
X-RAY DIFFRACTIONf_dihedral_angle_d11.793752
X-RAY DIFFRACTIONf_chiral_restr0.063293
X-RAY DIFFRACTIONf_plane_restr0.003329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4477-1.48390.38731330.35632211X-RAY DIFFRACTION90
1.4839-1.5240.35291390.26522324X-RAY DIFFRACTION94
1.524-1.56880.23511400.21412334X-RAY DIFFRACTION95
1.5688-1.61940.26391410.19662347X-RAY DIFFRACTION95
1.6194-1.67720.26121410.19952369X-RAY DIFFRACTION96
1.6772-1.74420.20861430.19492375X-RAY DIFFRACTION97
1.7442-1.82350.23991430.1872387X-RAY DIFFRACTION97
1.8235-1.91940.2171450.19062429X-RAY DIFFRACTION98
1.9194-2.03940.20351460.18792418X-RAY DIFFRACTION98
2.0394-2.19640.22371470.18122457X-RAY DIFFRACTION99
2.1964-2.41660.21470.18222459X-RAY DIFFRACTION99
2.4166-2.76430.21061490.19552470X-RAY DIFFRACTION99
2.7643-3.47540.23531470.17582448X-RAY DIFFRACTION98
3.4754-14.86070.17461390.16232328X-RAY DIFFRACTION91

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