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- PDB-4hco: Human Plk1-PBD in complex with Thymoquinone at the phophopeptide ... -

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Basic information

Entry
Database: PDB / ID: 4hco
TitleHuman Plk1-PBD in complex with Thymoquinone at the phophopeptide binding site
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / 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 / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / protein localization to nuclear envelope / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / double-strand break repair via alternative nonhomologous end joining / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / 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 / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / positive regulation of proteolysis / mitotic cytokinesis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / protein localization to chromatin / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / 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 / peptidyl-serine phosphorylation / microtubule binding / regulation of cell cycle / protein kinase activity / protein ubiquitination / 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
Chem-IMW / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYin, Z. / Rehse, P.H.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Thymoquinone Blocks pSer/pThr Recognition by Plk1 Polo-Box Domain As a Phosphate Mimic
Authors: Yin, Z. / Song, Y. / Rehse, P.H.
History
DepositionOct 1, 2012Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 10, 2012ID: 4H70
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Serine/threonine-protein kinase PLK1
A: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3454
Polymers55,0892
Non-polymers2562
Water1,856103
1
B: Serine/threonine-protein kinase PLK1


Theoretical massNumber of molelcules
Total (without water)27,5441
Polymers27,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8013
Polymers27,5441
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.260, 102.150, 67.740
Angle α, β, γ (deg.)90.00, 93.96, 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: 27544.373 Da / Num. of mol.: 2 / Fragment: UNP residues 367-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53350, polo kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMW / 2-methyl-5-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione / Thymoquinone / 2-isopropyl-5-methylbenzo-1,4-quinone


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.4M Sodium Potassium Tartrate, 50mM MES pH 6.5, 100mM Hepes pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→51.07 Å / Num. obs: 11125 / % possible obs: 94.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 5.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1551 / % possible all: 91.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UMW

1umw


Resolution: 2.75→51.07 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.797 / SU B: 18.386 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 531 4.8 %RANDOM
Rwork0.20588 ---
obs0.20956 10576 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.04 Å2
2--0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.75→51.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 18 103 3640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223609
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9744881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40222.988164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75815628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3121529
X-RAY DIFFRACTIONr_chiral_restr0.0760.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212699
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3741.52187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71123515
X-RAY DIFFRACTIONr_scbond_it0.89631422
X-RAY DIFFRACTIONr_scangle_it1.5114.51366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 33 -
Rwork0.286 754 -
obs--90.25 %

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