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- PDB-5dnj: Mouse Polo-box domain and Peptide analog 702 -

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Basic information

Entry
Database: PDB / ID: 5dnj
TitleMouse Polo-box domain and Peptide analog 702
Components
  • Serine/threonine-protein kinase PLK1
  • peptide 707-56A-SER-TPO-NH2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PLK1 / Emi2 / Protein Kinase / meiosis / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / Condensation of Prophase Chromosomes / polar body extrusion after meiotic divisions ...Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / Condensation of Prophase Chromosomes / polar body extrusion after meiotic divisions / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / protein localization to organelle / regulation of protein localization to cell cortex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / synaptonemal complex disassembly / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases Activate Formins / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase / nuclear membrane disassembly / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / synaptonemal complex / Regulation of PLK1 Activity at G2/M Transition / female meiosis chromosome segregation / anaphase-promoting complex binding / outer kinetochore / condensed chromosome, centromeric region / double-strand break repair via alternative nonhomologous end joining / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / centriolar satellite / spindle midzone / protein localization to chromatin / regulation of mitotic cell cycle / centriole / mitotic spindle organization / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / spindle microtubule / protein destabilization / establishment of protein localization / kinetochore / spindle / spindle pole / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / protein ubiquitination / 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 / ATP binding / identical protein binding / nucleus / 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
peptide inhibitor / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsNamgoong, S. / Han, Y.H.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for recognition of Emi2 by Polo-like kinase 1 and development of peptidomimetics blocking oocyte maturation and fertilization.
Authors: Jia, J.L. / Han, Y.H. / Kim, H.C. / Ahn, M. / Kwon, J.W. / Luo, Y. / Gunasekaran, P. / Lee, S.J. / Lee, K.S. / Bang, J.K. / Kim, N.H. / Namgoong, S.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: 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
B: peptide 707-56A-SER-TPO-NH2


Theoretical massNumber of molelcules
Total (without water)28,1372
Polymers28,1372
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-6 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.149, 59.989, 67.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 27242.980 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 367-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plk1, Plk / Production host: Escherichia coli (E. coli) / References: UniProt: Q07832, polo kinase
#2: Protein/peptide peptide 707-56A-SER-TPO-NH2


Type: PolypeptidePeptide / Class: Enzyme inhibitor / Mass: 893.738 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: peptide inhibitor
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% 2-propanol, 3% PEG 200, 0.1 M Bis-Tris (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 20, 2014
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.7 Å / Num. obs: 9156 / % possible obs: 90.4 % / Redundancy: 3.6 % / Net I/σ(I): 23.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.3→44.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.878 / SU B: 8.572 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27693 466 4.8 %RANDOM
Rwork0.19603 ---
obs0.19983 9156 90.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.458 Å2
Baniso -1Baniso -2Baniso -3
1--3.25 Å2-0 Å2-0 Å2
2--0.9 Å2-0 Å2
3---2.35 Å2
Refinement stepCycle: 1 / Resolution: 2.3→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 0 11 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021806
X-RAY DIFFRACTIONr_bond_other_d0.0060.021688
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9922442
X-RAY DIFFRACTIONr_angle_other_deg2.2523.0073872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47424.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01415301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3011510
X-RAY DIFFRACTIONr_chiral_restr0.1560.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022001
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02418
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_it2.3953.058870
X-RAY DIFFRACTIONr_mcbond_other2.3863.057868
X-RAY DIFFRACTIONr_mcangle_it3.9024.5741078
X-RAY DIFFRACTIONr_mcangle_other3.9024.5741079
X-RAY DIFFRACTIONr_scbond_it3.5253.539936
X-RAY DIFFRACTIONr_scbond_other3.5233.539937
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6775.1441365
X-RAY DIFFRACTIONr_long_range_B_refined7.73924.8731979
X-RAY DIFFRACTIONr_long_range_B_other7.73424.8791979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.305→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 24 -
Rwork0.264 566 -
obs--76.82 %

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