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- PDB-6ax4: Plk-1 polo-box domain in complex with histidine N(tau)-cyclized M... -

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Basic information

Entry
Database: PDB / ID: 6ax4
TitlePlk-1 polo-box domain in complex with histidine N(tau)-cyclized Macrocycle 5b.
Components
  • Serine/threonine-protein kinase PLK1
  • histidine N(tau)-cyclized Macrocycle 5b
KeywordsPROTEIN BINDING / macrocyclic phosphopeptide / mitotic kinase. polo-box domain
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 / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / 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 / mitotic sister chromatid segregation / 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
AMYLAMINE / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsGrant, R.A. / Hymel, D. / Yaffe, M.B. / Burke, T.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01-ES015339-06 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIA BC 006198 United States
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Histidine N( tau )-cyclized macrocycles as a new genre of polo-like kinase 1 polo-box domain-binding inhibitors.
Authors: Hymel, D. / Grant, R.A. / Tsuji, K. / Yaffe, M.B. / Burke Jr., T.R.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
C: histidine N(tau)-cyclized Macrocycle 5b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2363
Polymers28,1492
Non-polymers871
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-4 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.449, 51.294, 58.034
Angle α, β, γ (deg.)90.000, 100.840, 90.000
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: UNP residues 367-603
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 histidine N(tau)-cyclized Macrocycle 5b


Mass: 863.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AML / AMYLAMINE / 1-Aminopentane


Mass: 87.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.9 Å3/Da / Density % sol: 35.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Well solution: 0.2 M Calcium Chloride, 12.5% PEG-3350 Protein: 10 mg/ml PBD-macrocycle complex in 0.5 M Sodium Chloride, 10 mM TRIS pH 8.0, 0.4 M ammonium acetate 1:1 mix of protein complex and well solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.45→17.408 Å / Num. obs: 36144 / % possible obs: 99.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.88 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Χ2: 1.14 / Net I/σ(I): 8.6 / Num. measured all: 196289
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.484.60.62817970.7690.3260.7090.51199.1
1.48-1.550.59617510.80.2930.6650.53598.7
1.5-1.535.30.518110.8690.2380.5540.56599
1.53-1.565.40.41717890.9130.1960.4620.60699.2
1.56-1.65.50.36318060.9290.1680.4010.62199.2
1.6-1.635.50.31717730.9440.1470.350.65299.2
1.63-1.675.50.26218060.9610.1210.2890.65599.4
1.67-1.725.50.22417970.9690.1040.2470.70799.5
1.72-1.775.60.18418140.9760.0850.2030.76199.4
1.77-1.835.60.15717930.9810.0730.1730.8399.7
1.83-1.895.50.12618010.9890.0580.1390.90199.8
1.89-1.975.60.10418360.990.0480.1151.06199.8
1.97-2.065.60.08617910.9920.040.0951.1699.9
2.06-2.175.60.07418200.9950.0340.0811.37599.9
2.17-2.35.60.06818290.9950.0320.0751.525100
2.3-2.485.60.06817950.9950.0310.0751.735100
2.48-2.735.50.06218450.9960.0290.0691.97299.9
2.73-3.125.40.05418280.9960.0250.062.13999.9
3.12-3.945.50.04518370.9980.0210.052.25399.8
3.94-1005.30.04118250.9970.020.0461.96496.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dfw

4dfw


Resolution: 1.45→17.408 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.1
RfactorNum. reflection% reflection
Rfree0.1656 2000 5.54 %
Rwork0.1319 --
obs0.1338 36127 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.82 Å2 / Biso mean: 23.217 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.45→17.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 137 268 2205
Biso mean--23.11 32.85 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091935
X-RAY DIFFRACTIONf_angle_d1.0482625
X-RAY DIFFRACTIONf_chiral_restr0.08289
X-RAY DIFFRACTIONf_plane_restr0.005345
X-RAY DIFFRACTIONf_dihedral_angle_d16.284767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4492-1.48540.23461370.16262336247396
1.4854-1.52550.20861420.14952409255199
1.5255-1.57040.18271400.13492416255699
1.5704-1.62110.22211430.12992440258399
1.6211-1.6790.20911440.12642442258699
1.679-1.74610.17881410.122923982539100
1.7461-1.82550.16751430.111524502593100
1.8255-1.92160.14211420.112724312573100
1.9216-2.04190.17561450.110724552600100
2.0419-2.19920.16051430.111424532596100
2.1992-2.420.1671440.122524592603100
2.42-2.7690.17581450.137824682613100
2.769-3.48410.16491450.139624822627100
3.4841-17.40940.14141460.14692488263499

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