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- PDB-7mx1: PLK-1 polo-box domain in complex with a high affinity macrocycle ... -

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Basic information

Entry
Database: PDB / ID: 7mx1
TitlePLK-1 polo-box domain in complex with a high affinity macrocycle synthesized using a novel glutamic acid analog
Components
  • ACE-PRO-LEU-ALA-SER-TPO
  • Serine/threonine-protein kinase PLK1
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 / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope / Phosphorylation of Emi1 ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / nuclear membrane disassembly / synaptonemal complex / female meiosis chromosome segregation / Golgi inheritance / Phosphorylation of the APC/C / anaphase-promoting complex binding / outer kinetochore / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / mitotic chromosome condensation / Polo-like kinase mediated events / regulation of mitotic spindle assembly / 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 / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / mitotic cytokinesis / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / positive regulation of proteolysis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / centriole / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / regulation of cytokinesis / AURKA Activation by TPX2 / mitotic spindle organization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / RHO GTPases Activate Formins / protein destabilization / kinetochore / centriolar satellite / positive regulation of protein localization to nucleus / spindle / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / spindle pole / Regulation of PLK1 Activity at G2/M Transition / G2/M transition of mitotic cell cycle / peptidyl-serine phosphorylation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / microtubule cytoskeleton / midbody / microtubule binding / protein ubiquitination / protein kinase activity / regulation of cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process / protein kinase binding / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase 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. / 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
Similarity search - Domain/homology
Chem-ZOY / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGrant, R.A. / Hymel, D. / Yaffe, M.B. / Burke, T.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Org.Biomol.Chem. / Year: 2021
Title: Design and synthesis of a new orthogonally protected glutamic acid analog and its use in the preparation of high affinity polo-like kinase 1 polo-box domain - binding peptide macrocycles.
Authors: Hymel, D. / Tsuji, K. / Grant, R.A. / Chingle, R.M. / Kunciw, D.L. / Yaffe, M.B. / Burke Jr., T.R.
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Serine/threonine-protein kinase PLK1
C: ACE-PRO-LEU-ALA-SER-TPO
E: ACE-PRO-LEU-ALA-SER-TPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4806
Polymers55,7574
Non-polymers7232
Water8,467470
1
A: Serine/threonine-protein kinase PLK1
C: ACE-PRO-LEU-ALA-SER-TPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2403
Polymers27,8792
Non-polymers3621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area11430 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PLK1
E: ACE-PRO-LEU-ALA-SER-TPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2403
Polymers27,8792
Non-polymers3621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.713, 64.958, 71.674
Angle α, β, γ (deg.)90.000, 101.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 372 through 431 or resid 433 through 577 or resid 579 through 593))
21(chain B and (resid 372 through 431 or resid 433...
12chain C
22chain E
13chain D
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 372 through 431 or resid 433 through 577 or resid 579 through 593))A372 - 431
121(chain A and (resid 372 through 431 or resid 433 through 577 or resid 579 through 593))A433 - 577
131(chain A and (resid 372 through 431 or resid 433 through 577 or resid 579 through 593))A579 - 593
211(chain B and (resid 372 through 431 or resid 433...B372 - 431
221(chain B and (resid 372 through 431 or resid 433...B433 - 503
231(chain B and (resid 372 through 431 or resid 433...B506 - 577
241(chain B and (resid 372 through 431 or resid 433...B579 - 593
112chain CC0 - 5
212chain EE0 - 5
113chain DD1
213chain FF1

NCS ensembles :
ID
1
2
3

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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.: 2 / 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 ACE-PRO-LEU-ALA-SER-TPO


Mass: 593.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: no biological source / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZOY / N-[(4S)-4,5-diamino-5-oxopentyl]-10-phenyldecanamide


Mass: 361.522 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H35N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M. CaCl2, 15% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 62431 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Χ2: 1.14 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.717.21.15862200.6870.4621.2490.502100
1.71-1.787.40.75861990.8580.2990.8160.527100
1.78-1.867.40.49462220.9240.1940.5310.587100
1.86-1.967.50.33161920.9640.130.3560.804100
1.96-2.087.50.18762540.9850.0730.2010.908100
2.08-2.247.50.13562270.9910.0530.1451.141100
2.24-2.467.50.10762270.9930.0420.1151.373100
2.46-2.827.40.0862580.9950.0320.0861.581100
2.82-3.557.30.05562770.9980.0220.0592.00999.9
3.55-507.30.04263550.9980.0170.0451.96899.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DFW

4dfw


Resolution: 1.64→49.13 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 2000 3.2 %
Rwork0.1754 60411 -
obs0.1763 62411 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.69 Å2 / Biso mean: 45.6897 Å2 / Biso min: 11.81 Å2
Refinement stepCycle: final / Resolution: 1.64→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 118 470 4257
Biso mean--41.96 46.37 -
Num. residues----454
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms: 7.524 / Type: TORSIONAL

Ens-IDDom-IDAsym-IDAuth asym-IDNumber
11AA2072
12BB2072
21CC38
22DE38
31EC30
32FE30
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.64-1.690.2981200.2703362384
1.69-1.730.25381440.24834347100
1.73-1.780.29471430.22574343100
1.78-1.840.24881450.21164359100
1.84-1.910.21431444347100
1.91-1.980.24281440.21084351100
1.98-2.070.21751440.18514359100
2.07-2.180.1961440.18214363100
2.18-2.320.2171450.17694358100
2.32-2.50.19921450.17844382100
2.5-2.750.20971450.18354368100
2.75-3.140.22051450.17774373100
3.15-3.960.19341440.15864381100
3.96-49.130.17021480.1514445799
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)
12.67673.3087-0.08254.77660.62052.6487-0.1213-0.259-0.2160.42140.1466-0.14350.06930.0842-0.05580.2880.0087-0.02980.12980.04920.2449106.6811-20.622336.8817
27.44933.33712.5634.38611.21962.5870.0598-0.16560.3773-0.1052-0.00350.6508-0.1166-0.5266-0.1190.20370.00140.04790.23250.03850.251593.3807-10.308833.9132
34.3957-0.6508-0.59830.7754-0.99561.41290.0344-0.00580.40740.0303-0.0855-0.2389-0.02570.22510.0420.1925-0.0050.00190.1354-0.00190.2405126.0851-6.56625.59
46.41060.4952-1.37185.876-1.8164.1035-0.2383-0.59790.6496-0.214-0.1436-0.93920.53280.33840.17970.3288-0.0704-0.03880.36840.02670.361137.0607-7.824233.3155
56.3254-0.87930.56212.6359-0.23952.9938-0.12981.0870.8971-0.1275-0.2371-0.1748-0.44980.4940.25810.2308-0.04710.02240.29640.13310.3363133.003-2.900519.3385
63.6558-1.7944-1.59423.29051.45051.141-0.1349-0.31010.52540.5090.062-0.2184-0.29130.13390.06780.3076-0.0114-0.05220.1697-0.01550.3116116.0047-1.058131.8965
78.3272.58551.71286.42583.29094.3239-0.03670.3702-0.39520.08280.0688-0.32210.25980.22-0.14970.21950.02720.01850.1027-0.00920.1925117.2171-16.677723.3838
84.0458-1.4985-0.50892.8944-1.07560.84940.05310.3104-0.09350.003-0.03760.16750.0573-0.0827-0.02270.1708-0.0004-0.00810.1121-0.00490.1402110.457-11.208124.7452
94.2131-0.90760.1046.2435-2.75071.61080.03680.30990.3552-0.1827-0.10280.2124-0.04510.0089-0.00350.19250.01930.00670.11550.01040.168104.933-6.526827.8975
104.8749-0.4435-1.55573.32610.6042.467-0.03660.0686-0.28860.00410.01560.17890.2315-0.16120.01730.1948-0.0201-0.01590.09390.02380.1455102.6058-15.861230.2589
116.39590.9840.53541.5455-0.49280.2864-0.32281.2686-0.3498-1.16860.3468-0.08770.63180.36820.50920.5773-0.18030.28430.9071-0.13590.2303131.6259-10.723149.881
124.83710.7841-0.14471.2575-0.86942.959-0.24030.34310.2069-0.04260.0923-0.05470.1060.14650.070.1877-0.00670.00390.31360.07020.234124.0996-2.871462.9898
133.1671-0.3779-0.26761.4313-0.39084.0522-0.10090.87750.81510.12220.096-0.01070.438-0.9201-0.27810.26410.05690.07140.81770.29940.4243103.72752.354559.1266
142.9744-1.75432.09991.6727-1.78211.9745-0.2147-0.97710.28770.41490.26030.0609-0.5022-1.42040.12670.27990.13380.06770.72660.08510.3008105.91260.016372.2359
153.76061.8267-1.73433.3714-1.7314.07910.1006-0.74920.84680.3744-0.23730.1946-0.3828-0.32390.11270.2745-0.084-0.03360.4702-0.06350.3756126.61865.937269.3794
162.5421-1.07010.66229.3191-3.69324.32-0.12160.35210.1794-0.1717-0.0976-0.07480.1301-0.10260.12340.1861-0.0121-0.01330.32680.05580.1829119.8806-3.871859.8234
174.96420.71020.1193.31980.96583.6882-0.05480.02260.00690.13950.0415-0.20420.05150.5023-0.02420.2261-0.0028-0.02060.41510.1090.231130.8388-3.729163.9303
187.9414-2.4121-2.45773.74140.48644.40170.02060.57640.1836-0.4835-0.2445-0.3933-0.00160.40010.09940.3361-0.04710.02520.72540.15970.3724141.4273-1.6155.494
192.29651.4863-0.63783.4107-1.7932.5096-0.55290.096-1.483-0.2235-0.1495-0.80441.09870.6280.32810.40130.06640.1820.40950.02830.4845132.4161-14.273559.3322
202.6888-3.0188-4.02587.82866.85237.25480.09910.0053-0.19060.5073-0.15160.4651.0349-0.19660.43960.2860.0652-0.00980.29420.10340.1744120.4974-9.809912.61
213.595-3.89650.40954.55280.33063.79450.2008-0.0167-0.2018-0.1212-0.07050.10450.4243-0.11630.01560.29320.04540.00470.49040.03950.2837120.1344-8.657275.7985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 372 through 387 )A372 - 387
2X-RAY DIFFRACTION2chain 'A' and (resid 388 through 405 )A388 - 405
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 454 )A406 - 454
4X-RAY DIFFRACTION4chain 'A' and (resid 455 through 469 )A455 - 469
5X-RAY DIFFRACTION5chain 'A' and (resid 470 through 489 )A470 - 489
6X-RAY DIFFRACTION6chain 'A' and (resid 490 through 510 )A490 - 510
7X-RAY DIFFRACTION7chain 'A' and (resid 511 through 525 )A511 - 525
8X-RAY DIFFRACTION8chain 'A' and (resid 526 through 544 )A526 - 544
9X-RAY DIFFRACTION9chain 'A' and (resid 545 through 558 )A545 - 558
10X-RAY DIFFRACTION10chain 'A' and (resid 559 through 593 )A559 - 593
11X-RAY DIFFRACTION11chain 'B' and (resid 372 through 386 )B372 - 386
12X-RAY DIFFRACTION12chain 'B' and (resid 387 through 444 )B387 - 444
13X-RAY DIFFRACTION13chain 'B' and (resid 445 through 469 )B445 - 469
14X-RAY DIFFRACTION14chain 'B' and (resid 470 through 489 )B470 - 489
15X-RAY DIFFRACTION15chain 'B' and (resid 490 through 499 )B490 - 499
16X-RAY DIFFRACTION16chain 'B' and (resid 500 through 525 )B500 - 525
17X-RAY DIFFRACTION17chain 'B' and (resid 526 through 558 )B526 - 558
18X-RAY DIFFRACTION18chain 'B' and (resid 559 through 573 )B559 - 573
19X-RAY DIFFRACTION19chain 'B' and (resid 574 through 593 )B574 - 593
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 4 )C1 - 4
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 4 )E1 - 4

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