5lhz

PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL

Method: X-RAY DIFFRACTION D_max: 86.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase PLK4

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 884–970	Fragment：UNP residues 884-970	SCL-interrupting locus protein × 1 （Q15468）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 884–970	Fragment：UNP residues 884-970	SCL-interrupting locus protein × 1 （Q15468）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 884–970	Fragment：UNP residues 884-970	SCL-interrupting locus protein × 1 （Q15468）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5LHZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N19 STIL binding to the Polo-box domain 3 of PLK4 regulates centriole duplication Deposited 2015-03-24	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293.15 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient NMR sample composition 0.6-1.2 M [U-13C; U-15N; U-2H] PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6-1.2 M [U-2H,15N,methyl13C/rest-12C-ILV]-PB3 PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1200 mM [U-2H,15N,13C,methyl13C/1H-ILV]-PB3 PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 600 mM [U-2H, U-15N] PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3COK Crystal structure of PLK4 kinase Deposited 2008-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa） Fragment：Protein kinase domain: Residues 2-275	Not recorded	SO4 SULFATE ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；100mM Sodium citrate pH 6.0, 16% PEG 4000, 200mM Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.25 Å R-free 0.261
3COK Crystal structure of PLK4 kinase Deposited 2008-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–275（274 aa） Fragment：Protein kinase domain: Residues 2-275	Not recorded	SO4 SULFATE ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；100mM Sodium citrate pH 6.0, 16% PEG 4000, 200mM Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.25 Å R-free 0.261
4JXF Crystal Structure of PLK4 Kinase with an inhibitor: 400631 ((1R,2S)-2-{3-[(E)-2-{4-[(DIMETHYLAMINO)METHYL]PHENYL}ETHENYL]-2H-INDAZOL-6-YL}-5'-METHOXYSPIRO[CYCLOPROPANE-1,3'-INDOL]-2'(1'H)-ONE) Deposited 2013-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–269（266 aa） Fragment：PLK4 kinase	Not recorded	631 (1R,2S)-2-{3-[(E)-2-{4-[(dimethylamino)methyl]phenyl}ethenyl]-2H-indazol-6-yl}-5'-methoxyspiro[cyclopropane-1,3'-indol]-2'(1'H)-one × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；23% PEG 3350, 0.1 M HEPES pH 7.5 0.16 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.268
4N7V Crystal structure of human Plk4 cryptic polo box (CPB) in complex with a Cep152 N-terminal fragment Deposited 2013-10-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 580–808（229 aa） Fragment：UNP residues 580-808 Chain B 580–808（229 aa） Fragment：UNP residues 580-808	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295.15 K；22% PEG 4000, 3% Iso-propanol, 0.1M Tris-HCl, 0.2M Lithium Sulfate , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 2.76 Å R-free 0.288
4N7Z Crystal structure of human Plk4 cryptic polo box (CPB) in complex with a Cep192 N-terminal fragment Deposited 2013-10-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 580–808（229 aa） Fragment：UNP residues 580-808	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；20% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 2.85 Å R-free 0.260
4N9J Crystal structure of the cryptic polo box domain of human Plk4 Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Fragment：cryptic polo box, UNP residues 580-808 Chain B 581–808（228 aa） Fragment：cryptic polo box, UNP residues 580-808	Not recorded	CL CHLORIDE ION × 6 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；100 mM Bis-Tris (pH 5.5), 2.0 M ammonium sulfate, 1% (v/v) methanol , VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.60 Å R-free 0.249
4YUR Crystal Structure of Plk4 Kinase Domain Bound to Centrinone Deposited 2015-03-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa） Fragment：UNP residues 2-275	Not recorded	4J7 2-({2-fluoro-4-[(2-fluoro-3-nitrobenzyl)sulfonyl]phenyl}sulfanyl)-5-methoxy-N-(3-methyl-1H-pyrazol-5-yl)-6-(morpholin-4-yl)pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1 M HEPES, 0.2 M MgCl2, 30% PEG 400	Resolution 2.65 Å R-free 0.270
4YYP Crystal structure of human PLK4-PB3 in complex with STIL-CC Deposited 2015-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 884–970（87 aa） Fragment：residues 884-970	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Thin needles grew in precipitant solution containing 100 mM Hepes, pH 7.0, 20 mM MgCl2 and 22% Poly(acrylic acid sodium salt) 5100. After extensive optimization and seeding plate-like crystals were grown in a drop consisting of 50% PLK4-PB3/STIL-CC complex solution, 33.3% precipitant solution (100 mM phosphate/citrate pH 4.2, 40% (v/v) Ethanol, 5% (w/v) PEG 1000) and 16.7% of seed stock solution.	Resolution 2.60 Å R-free 0.254
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 884–970（87 aa） Fragment：UNP residues 884-970 Chain B 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain S 884–970（87 aa） Fragment：UNP residues 884-970 Chain T 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 11 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain U 884–970（87 aa） Fragment：UNP residues 884-970 Chain V 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 12 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain W 884–970（87 aa） Fragment：UNP residues 884-970 Chain X 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 13 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain Y 884–970（87 aa） Fragment：UNP residues 884-970 Chain Z 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 14 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 884–970（87 aa） Fragment：UNP residues 884-970 Chain 2 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 15 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 3 884–970（87 aa） Fragment：UNP residues 884-970 Chain 4 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 16 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 5 884–970（87 aa） Fragment：UNP residues 884-970 Chain 6 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 17 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 7 884–970（87 aa） Fragment：UNP residues 884-970 Chain 8 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 18 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 9 884–970（87 aa） Fragment：UNP residues 884-970 Chain a 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 19 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain b 884–970（87 aa） Fragment：UNP residues 884-970 Chain c 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 884–970（87 aa） Fragment：UNP residues 884-970 Chain D 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 20 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain d 884–970（87 aa） Fragment：UNP residues 884-970 Chain e 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 21 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain f 884–970（87 aa） Fragment：UNP residues 884-970 Chain g 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 22 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain h 884–970（87 aa） Fragment：UNP residues 884-970 Chain i 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 23 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain j 884–970（87 aa） Fragment：UNP residues 884-970 Chain k 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 24 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain l 884–970（87 aa） Fragment：UNP residues 884-970 Chain m 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 25 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain n 884–970（87 aa） Fragment：UNP residues 884-970 Chain o 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 26 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain p 884–970（87 aa） Fragment：UNP residues 884-970 Chain q 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 27 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain r 884–970（87 aa） Fragment：UNP residues 884-970 Chain s 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 28 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain t 884–970（87 aa） Fragment：UNP residues 884-970 Chain u 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 29 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain v 884–970（87 aa） Fragment：UNP residues 884-970 Chain w 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 884–970（87 aa） Fragment：UNP residues 884-970 Chain F 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 30 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain x 884–970（87 aa） Fragment：UNP residues 884-970 Chain y 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 884–970（87 aa） Fragment：UNP residues 884-970 Chain H 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 884–970（87 aa） Fragment：UNP residues 884-970 Chain J 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 884–970（87 aa） Fragment：UNP residues 884-970 Chain L 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 884–970（87 aa） Fragment：UNP residues 884-970 Chain N 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 884–970（87 aa） Fragment：UNP residues 884-970 Chain P 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain Q 884–970（87 aa） Fragment：UNP residues 884-970 Chain R 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
6N45 Crystal structure of the cryptic polo box domain of human activated Plk4 variant 1 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Chain B 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；4.3M Ammonium Acetate 0.1M BisTris propane pH 8.0	Resolution 2.64 Å R-free 0.314
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Chain B 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 581–808（228 aa） Chain D 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 581–808（228 aa） Chain F 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 581–808（228 aa） Chain H 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6W38 Crystal structure of the FAM46C/Plk4 complex Deposited 2020-03-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 585–807（223 aa） Fragment：UNP residues 585-807	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 10；293 K；0.2 M Tris, pH 10	Resolution 4.48 Å R-free 0.295
6W3I Crystal structure of a FAM46C mutant in complex with Plk4 Deposited 2020-03-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 585–807（223 aa） Fragment：UNP residues 585-807	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% v/v pentaerythritol ethoxylate (15/4 EO/OH), 0.05 M ammonium sulfate, 0.05 M Bis-Tris, pH 6.0	Resolution 3.80 Å R-free 0.261
6W3J Crystal structure of the FAM46C/Plk4/Cep192 complex Deposited 2020-03-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 585–807（223 aa） Fragment：UNP residues 585-807	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 10；293 K；0.2 M Tris, pH 10	Resolution 4.38 Å R-free 0.314
8XPG The Crystal Structure of polo box domain of Plk4 from Biortus. Deposited 2024-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Chain B 581–808（228 aa）	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.00M Ammonium sulfate, 100mM TRIS, pH7.0, 200mM Lithium sulfate	Resolution 2.70 Å R-free 0.260
9O63 Crystal structure of PLK4 and RP1664 complex Deposited 2025-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa）	Not recorded	SO4 SULFATE ION × 2 A1CAD 5-cyclopropyl-N~2~-[2,6-difluoro-4-(methanesulfonyl)phenyl]-N~2~-methyl-6-(1-methyl-1H-imidazol-4-yl)-N~4~-(5-methyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；9 - 14% PEG4K, 0.1 M Na Cit; pH 5.4 - 5.5, 0.2 M (NH4)2SO4	Resolution 2.26 Å R-free 0.264
9Y9B PLK4 in complex with Compound 6 (3-hydroxy-N-(3-(pyridin-2-yl)-1H-pyrazol-4-yl)-8-azabicyclo[3.2.1]octane-8-carboxamide) Deposited 2025-09-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa）	Not recorded	SO4 SULFATE ION × 1 A1CTX (1R,3r,5S)-3-hydroxy-N-[3-(pyridin-2-yl)-1H-pyrazol-4-yl]-8-azabicyclo[3.2.1]octane-8-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；0.1 M Tris pH 8.5, 16% ethanol , 5 mM DTT	Resolution 2.70 Å R-free 0.335
9Y9N PLK4 in complex with Compound 25 ((R)-7-hydroxy-N-(3-(1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl)-1H-pyrazol-4-yl)-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide) Deposited 2025-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–269（266 aa）	Not recorded	A1CTV (7R)-7-hydroxy-N-{(5P)-5-[1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-1H-pyrazol-4-yl}-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；1.4 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic pH 5.6	Resolution 1.81 Å R-free 0.237

18 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLK4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–91； UniProt 884–970 Author chain B； PDBConstruct 5–91； UniProt 884–970 Author chain C； PDBConstruct 5–91； UniProt 884–970

SCL-interrupting locus protein

Homo sapiens

UniProt Q15468

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 726–750	Fragment：UNP residues 726-750	Serine/threonine-protein kinase PLK4 × 1 （O00444）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 726–750	Fragment：UNP residues 726-750	Serine/threonine-protein kinase PLK4 × 1 （O00444）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 726–750	Fragment：UNP residues 726-750	Serine/threonine-protein kinase PLK4 × 1 （O00444）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5LHZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4YYP Crystal structure of human PLK4-PB3 in complex with STIL-CC Deposited 2015-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 720–751（32 aa） Fragment：residues 720-751	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Thin needles grew in precipitant solution containing 100 mM Hepes, pH 7.0, 20 mM MgCl2 and 22% Poly(acrylic acid sodium salt) 5100. After extensive optimization and seeding plate-like crystals were grown in a drop consisting of 50% PLK4-PB3/STIL-CC complex solution, 33.3% precipitant solution (100 mM phosphate/citrate pH 4.2, 40% (v/v) Ethanol, 5% (w/v) PEG 1000) and 16.7% of seed stock solution.	Resolution 2.60 Å R-free 0.254
5LHW Central Coiled-Coil Domain of Human STIL Deposited 2016-07-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 726–750（25 aa） Fragment：UNP residues 726-750	Not recorded	P6G HEXAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；292 K；150 nl protein solution (58.6 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM TCEP) and 150 nl of mother liquor (7 mM HEPES pH 8.2, 93 mM Tris pH 9.0, 55.36% v/v PEG 550 MME, 10% v/v glycerol)	Resolution 0.91 Å R-free 0.139
8OYK Coiled-Coil Domain of Human STIL, L736E Mutant Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 718–749（32 aa） Chain B 718–749（32 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；0.9 mM peptide, 50 mM Tris, and 10 % v/v MPD, at pH 8.0.	Resolution 1.90 Å R-free 0.225
8OYK Coiled-Coil Domain of Human STIL, L736E Mutant Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 718–749（32 aa） Chain E 718–749（32 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；0.9 mM peptide, 50 mM Tris, and 10 % v/v MPD, at pH 8.0.	Resolution 1.90 Å R-free 0.225
8OYK Coiled-Coil Domain of Human STIL, L736E Mutant Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 718–749（32 aa） Chain F 718–749（32 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；0.9 mM peptide, 50 mM Tris, and 10 % v/v MPD, at pH 8.0.	Resolution 1.90 Å R-free 0.225
8OYL Coiled-Coil Domain of Human STIL, Q729L Mutant Deposited 2023-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 718–749（32 aa）	Not recorded	NA SODIUM ION × 4 CD CADMIUM ION × 8 CL CHLORIDE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；1.5 mM peptide, 50 mM Cadmium chloride hemi(pentahydrate), 50 mM Sodium acetate, and 15 % v/v PEG 400, at pH 4.6	Resolution 1.92 Å R-free 0.190

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STIL_HUMAN
Isoform	Q15468-2
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 4–28； UniProt 726–750 Author chain E； PDBConstruct 4–28； UniProt 726–750 Author chain F； PDBConstruct 4–28； UniProt 726–750

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lhz
Deposition date deposition_date	2016-07-13
Structure title title	PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL
Keywords keywords	Polo box domain, Centriole, Complex, transferase, structural protein; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.19 Å
Radius of gyration Rg (electron density) rg_electron	26.73 Å
Forward intensity I(0) i0	18074000.00
Molecular weight molecular_weight	33242.0 kDa
Excluded volume excluded_volume	41997 Å³
Envelope volume envelope_volume	56597 Å³
Hydration-shell volume shell_volume	18619 Å³
Envelope diameter envelope_diameter	89.2 Å
Shell Rg shell_rg	32.21 Å
Envelope Rg envelope_rg	26.15 Å
Shape Rg shape_rg	26.75 Å
Total Rg total_rg	27.34 Å
Total atoms total_atoms	4726
Residues n_residues	296
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	86.9 Å
Rg (real space) rg_real	27.35 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.8070e+07
I(0) uncertainty (real space) i0_real_error	2.9160e+05
Rg (reciprocal space) rg_reciprocal	27.31 Å
I(0) (reciprocal space) i0_reciprocal	18070000.0000
Solution quality estimate total_estimate	0.8329
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.303
Kurtosis Kurtosis kurtosis	-0.842
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6946000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.705; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.747; Smooth: 0.963

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Serine/threonine-protein kinase PLK4
Molecular weight formula_weight	9915.2 kDa
EC 编号 ec_number	2.7.11.21
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4731

GPMGSAQLLKSVFVKNVGWATQLTSGAVWVQFNDGSQLVVQAGVSSISYTSPNGQTTRYGENEKLPDYIKQKLQCLSSILLMFSNPTPNFH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli B

Entity 2 Entity 2 polymer

Description description	SCL-interrupting locus protein
Molecular weight formula_weight	3199.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

GGSLTEQDRQLRLLQAQIQRLLEAQSLM

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli B

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5lhza_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.223 — Polo-box domain
Superfamily Superfamily superfamily	d.223.1 — Polo-box domain
Family Family family	d.223.1.1 — Swapped Polo-box domain

Domain ID domain_id	d5lhzb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.223 — Polo-box domain
Superfamily Superfamily superfamily	d.223.1 — Polo-box domain
Family Family family	d.223.1.1 — Swapped Polo-box domain

Domain ID domain_id	d5lhzc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.223 — Polo-box domain
Superfamily Superfamily superfamily	d.223.1 — Polo-box domain
Family Family family	d.223.1.1 — Swapped Polo-box domain

CATH v4.4 (3 domains)

Domain ID domain_id	5lhzA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	30 — POLO box domain

Domain ID domain_id	5lhzB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	30 — POLO box domain

Domain ID domain_id	5lhzC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	30 — POLO box domain

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8. Citations (1)

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Unit-cell length a length_a	68.360 Å
Unit-cell length b length_b	68.360 Å
Unit-cell length c length_c	137.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	36.223 Å
R factor r_factor	0.2513
R_work r_work	0.2496
R_free r_free	0.2821

fit	/app/data/saxs_computation/lh/5lhz/5lhz.fit
pddf	/app/data/pr_computation/lh/5lhz/5lhz.pr.out
profile	/app/data/saxs_computation/lh/5lhz/5lhz.dat

PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL

1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase PLK4

State in the Current Structure

Other States of the Same Protein in the Database

SCL-interrupting locus protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)