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- PDB-3rq7: Polo-like kinase 1 Polo box domain in complex with a C6H5(CH2)8-d... -

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Basic information

Entry
Database: PDB / ID: 3rq7
TitlePolo-like kinase 1 Polo box domain in complex with a C6H5(CH2)8-derivatized peptide inhibitor
Components
  • C6H5(CH2)8-derivatized peptide inhibitor
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / phosphopeptide 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 / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase ...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 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase / nuclear membrane disassembly / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / anaphase-promoting complex binding / regulation of protein binding / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / double-strand break repair via alternative nonhomologous end joining / 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 / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / establishment of mitotic spindle orientation / mitotic cytokinesis / centriolar satellite / spindle midzone / 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 / regulation of mitotic cell cycle / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / 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 / spindle pole / positive regulation of protein localization to nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / 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 / magnesium ion binding / negative regulation of transcription by RNA polymerase II / 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
C6H5(CH2)8-derivatized peptide inhibitor / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLiu, F. / Park, J.-E. / Qian, W.-J. / Lim, D.C. / Graber, M. / Berg, T. / Yaffe, M.B. / Lee, K.S. / Burke Jr., T.R.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel.
Authors: Liu, F. / Park, J.E. / Qian, W.J. / Lim, D. / Graber, M. / Berg, T. / Yaffe, M.B. / Lee, K.S. / Burke, T.R.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Oct 10, 2012Group: Structure summary
Revision 1.4Dec 12, 2012Group: Other

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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)28,1312
Polymers28,1312
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.337, 51.210, 57.963
Angle α, β, γ (deg.)90.00, 101.00, 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
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 C6H5(CH2)8-derivatized peptide inhibitor


Type: PolypeptidePeptide / Class: Enzyme inhibitor / Mass: 845.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: C6H5(CH2)8-derivatized peptide inhibitor
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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
Details: PBD protein at 12 mg/mL in 10 mM Tris, pH 8.0, 0.5 M NaCl, 10 mM DTT, 2% DMSO and 2 mM compound 4j was mixed with an equal volume of reservoir solution consisting of 15% (w/v) PEG 3350, 0.1 ...Details: PBD protein at 12 mg/mL in 10 mM Tris, pH 8.0, 0.5 M NaCl, 10 mM DTT, 2% DMSO and 2 mM compound 4j was mixed with an equal volume of reservoir solution consisting of 15% (w/v) PEG 3350, 0.1 M glycine, pH 9.0, 300 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: Sep 30, 2009
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→14.814 Å / Num. all: 29483 / Num. obs: 29160 / % possible obs: 99.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4
Reflection shellResolution: 1.55→1.61 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→14.8 Å / SU ML: -0 / σ(F): 0.08 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 1454 4.99 %Random
Rwork0.152 ---
obs0.1539 29160 98.67 %-
all-29483 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.201 Å2 / ksol: 0.501 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 0 304 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123704
X-RAY DIFFRACTIONf_angle_d1.6656686
X-RAY DIFFRACTIONf_dihedral_angle_d17.02981
X-RAY DIFFRACTIONf_chiral_restr0.097273
X-RAY DIFFRACTIONf_plane_restr0.013536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60530.24491360.17552619X-RAY DIFFRACTION94
1.6053-1.66950.2241430.15872717X-RAY DIFFRACTION98
1.6695-1.74530.21231430.15412746X-RAY DIFFRACTION98
1.7453-1.83720.23211450.14762790X-RAY DIFFRACTION99
1.8372-1.95210.22381440.14682760X-RAY DIFFRACTION99
1.9521-2.10240.17861490.13222797X-RAY DIFFRACTION100
2.1024-2.31330.19751460.13272803X-RAY DIFFRACTION100
2.3133-2.64640.18081480.14052793X-RAY DIFFRACTION99
2.6464-3.32790.18291490.1372813X-RAY DIFFRACTION99
3.3279-14.81510.15871510.1632868X-RAY DIFFRACTION100

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