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- PDB-2rku: Structure of PLK1 in complex with BI2536 -

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Basic information

Entry
Database: PDB / ID: 2rku
TitleStructure of PLK1 in complex with BI2536
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / Structure of PLK1 / selectivity residues / kinase / polo-like kinase / structure based drug design / ATP-binding / Nucleotide-binding / Nucleus / Phosphorylation / Serine/threonine-protein kinase
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 / nuclear membrane disassembly / polo kinase / 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 / nuclear membrane disassembly / polo kinase / 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 / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / 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 / centriolar satellite / mitotic cytokinesis / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / establishment of protein localization / 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 / microtubule binding / peptidyl-serine phosphorylation / 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 / cytoplasm / cytosol
Similarity search - Function
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-R78 / S,R MESO-TARTARIC ACID / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsDing, Y.-H. / Kothe, M. / Kohls, D. / Low, S.
CitationJournal: Chem.Biol.Drug Des. / Year: 2007
Title: Selectivity-determining residues in Plk1.
Authors: Kothe, M. / Kohls, D. / Low, S. / Coli, R. / Rennie, G.R. / Feru, F. / Kuhn, C. / Ding, Y.-H.
History
DepositionOct 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,1618
Polymers33,8231
Non-polymers1,3377
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase PLK1
hetero molecules

A: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,32216
Polymers67,6472
Non-polymers2,67514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area4670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.593, 66.593, 154.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 33823.461 Da / Num. of mol.: 1 / Mutation: T210V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53350, polo kinase

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Non-polymers , 6 types, 292 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39N7O3
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.92 Å3/Da / Density % sol: 57.82 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 29527 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.069 / Χ2: 1.116 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.0260.50528880.982199.9
2.02-2.16.40.36628581.1511100
2.1-2.26.60.29429291.0851100
2.2-2.316.60.2829241.3041100
2.31-2.466.70.18529291.095199.9
2.46-2.656.70.13529131.0191100
2.65-2.916.80.09329511.0171100
2.91-3.336.90.06229781.031100
3.33-4.270.04630161.0931100
4.2-506.80.04431411.362199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.95→33.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.232 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1494 5.1 %RANDOM
Rwork0.19 ---
obs0.192 29416 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.011 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å21.18 Å20 Å2
2--2.37 Å20 Å2
3----3.55 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 89 285 2753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222558
X-RAY DIFFRACTIONr_angle_refined_deg1.4382.0143462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61922.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8915454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1631523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021929
X-RAY DIFFRACTIONr_nbd_refined0.1950.21119
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2265
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.216
X-RAY DIFFRACTIONr_mcbond_it0.8451.51550
X-RAY DIFFRACTIONr_mcangle_it1.35122446
X-RAY DIFFRACTIONr_scbond_it2.18531154
X-RAY DIFFRACTIONr_scangle_it3.524.51016
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 107 -
Rwork0.25 1943 -
all-2050 -
obs--95.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.661-2.05646.137213.071.666311.8916-1.7459-1.0295-0.9041-0.17020.71680.14120.082-1.68491.02910.3212-0.10870.26290.16780.1141-0.2158-40.2378-1.81073.8106
21.13980.6483-1.64252.5081-0.38166.1352-0.10770.1684-0.1163-0.0765-0.13250.17740.7831-0.29120.2402-0.1207-0.0590.0537-0.2169-0.0445-0.1699-41.96537.71236.7972
32.4487-0.0316-0.40161.75110.39365.6065-0.1138-0.0585-0.02820.16070.0579-0.13540.06410.24330.0559-0.27390.0325-0.0217-0.1477-0.0297-0.1498-35.271823.57219.3793
42.9048-0.5113-1.6760.98090.47926.4368-0.08990.17620.3805-0.10450.0733-0.1101-0.72220.07130.0165-0.1896-0.0112-0.0289-0.204-0.0139-0.1323-37.582434.377810.932
53.5222-0.06671.74782.14-0.06396.1711-0.3677-0.25990.668-0.02060.2258-0.1992-0.9117-0.31150.1419-0.12760.0167-0.0609-0.3127-0.0595-0.1448-42.026940.765918.409
64.08361.3720.73991.7111-0.17785.3953-0.01-0.5493-0.11860.5604-0.001-0.00220.25-0.39050.011-0.150.0589-0.0095-0.0682-0.0304-0.2162-40.491125.884237.3979
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA37 - 501 - 14
2X-RAY DIFFRACTION2AA51 - 10015 - 64
3X-RAY DIFFRACTION3AA151 - 200115 - 164
4X-RAY DIFFRACTION4AA201 - 250165 - 214
5X-RAY DIFFRACTION5AA251 - 294215 - 258
6X-RAY DIFFRACTION6AB - G501 - 5071

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