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6n45

Crystal structure of the cryptic polo box domain of human activated Plk4 variant 1

Method: X-RAY DIFFRACTION Dmax: 90.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chimera protein of Serine/threonine-protein kinase PLK4 and DDB1- and CUL4-associated factor 1

Homo sapiens

UniProt O00444

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 581–808 Chain B； UniProt 581–808 Not recorded No other associated polymer 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

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 6N45 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 construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 mutation/modification 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 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 mutation/modification 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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；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
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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；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
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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；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
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 53 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 5–232； UniProt 581–808 Author chain B； PDBConstruct 5–232； UniProt 581–808

Chimera protein of Serine/threonine-protein kinase PLK4 and DDB1- and CUL4-associated factor 1

Homo sapiens

UniProt Q9Y4B6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1475–1507 Chain B； UniProt 1475–1507 Not recorded No other associated polymer 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

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 6N45 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3WA0 Crystal structure of merlin complexed with DCAF1/VprBP Deposited 2013-04-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1417–1506（90 aa） Fragment：UNP residues 1417-1506
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.31 Å R-free 0.264
3WA0 Crystal structure of merlin complexed with DCAF1/VprBP Deposited 2013-04-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1417–1506（90 aa） Fragment：UNP residues 1417-1506
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.31 Å R-free 0.264
4CC9 Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396) Deposited 2013-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1058–1396（339 aa） Fragment：RESIDUES 1058-1396
Not recorded PG4 TETRAETHYLENE GLYCOL × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 15% PEG 400
Resolution 2.47 Å R-free 0.216
4P7I Crystal structure of the Merlin FERM/DCAF1 complex Deposited 2014-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 998–1058（61 aa） Fragment：UNP residues 998-1058
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% Isopropanol and 5% PEG8000
Resolution 2.60 Å R-free 0.256
4P7I Crystal structure of the Merlin FERM/DCAF1 complex Deposited 2014-03-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 998–1058（61 aa） Fragment：UNP residues 998-1058
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% Isopropanol and 5% PEG8000
Resolution 2.60 Å R-free 0.256
4PXW Crystal structure of human DCAF1 WD40 repeats (Q1250L) Deposited 2014-03-25 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L UNX UNKNOWN LIGAND × 22 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.72 Å R-free 0.219
4PXW Crystal structure of human DCAF1 WD40 repeats (Q1250L) Deposited 2014-03-25 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L UNX UNKNOWN LIGAND × 23 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.72 Å R-free 0.219
4Z8L Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex Deposited 2015-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1057–1396（340 aa） Fragment：UNP residues 1057-1396
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2
Resolution 2.60 Å R-free 0.228
4Z8L Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex Deposited 2015-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1057–1396（340 aa） Fragment：UNP residues 1057-1396
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2
Resolution 2.60 Å R-free 0.228
5AJA Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396) Deposited 2015-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1058–1396（339 aa） Fragment：WD40-REPEAT DOMAIN, RESIDUES 1058-1396
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.16 M TRISODIUM CITRATE-HCL PH 5.2, 4% PEG 6000
Resolution 2.65 Å R-free 0.227
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1045–1396（352 aa） Fragment：UNP residues 1045-1396
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
Resolution 3.49 Å R-free 0.206
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1045–1396（352 aa） Fragment：UNP residues 1045-1396
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
Resolution 3.49 Å R-free 0.206
6ZUE Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1046–1396（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；100 mM Tri-Na citrate pH 5.5 18% PEG 1000
Resolution 3.09 Å R-free 0.279
6ZX9 Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1046–1396（351 aa）
Not recorded GOL GLYCEROL × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.
Resolution 2.52 Å R-free 0.260
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: Hexadecameric
Chain B 2–1507（1506 aa）
Chain F 2–1507（1506 aa）
Chain J 2–1507（1506 aa）
Chain N 2–1507（1506 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7SSE Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70 Deposited 2021-11-10 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 1077–1390（314 aa）
Chain B 1077–1390（314 aa）
Mutation：F1077A, R1079A Mutation：F1077A, R1079A B1I N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；30% PEG3350 ,0.1M Ammonium Sulphate, 0.1M Bis-Tris pH5.5
Resolution 1.62 Å R-free 0.234
7UFV Crystal structure of the WDR domain of human DCAF1 in complex with OICR-6766 Deposited 2022-03-23 Different construct Different mutation/modification 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 1077–1390（314 aa）
Mutation：F1077A, R1079A N6O (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；20% PEG3350, 0.2M Potassium Fluoride
Resolution 1.90 Å R-free 0.254
7UFV Crystal structure of the WDR domain of human DCAF1 in complex with OICR-6766 Deposited 2022-03-23 Different construct Different mutation/modification 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 1077–1390（314 aa）
Mutation：F1077A, R1079A N6O (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；20% PEG3350, 0.2M Potassium Fluoride
Resolution 1.90 Å R-free 0.254
7V7B CryoEM structure of DDB1-VprBP complex in ARM-up conformation Deposited 2021-08-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1507（1507 aa）
Chain C 1–1507（1507 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7V7C CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex Deposited 2021-08-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–1507（1507 aa）
Chain E 1–1507（1507 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8F8E Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound Deposited 2022-11-21 Different construct Different mutation/modification 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 1077–1390（314 aa）
Mutation：F1077A, R1079A XJI (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M di-Ammonium Citrate
Resolution 1.55 Å R-free 0.209
8F8E Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound Deposited 2022-11-21 Different construct Different mutation/modification 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 1077–1390（314 aa）
Mutation：F1077A, R1079A XJI (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M di-Ammonium Citrate
Resolution 1.55 Å R-free 0.209
8OG5 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 Deposited 2023-03-19 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
Resolution 2.20 Å R-free 0.235
8OG6 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 Deposited 2023-03-19 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris pH 7.0, 2.13M Lithium acetate
Resolution 2.25 Å R-free 0.231
8OG7 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 2 Deposited 2023-03-19 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 VMR (4~{R})-4-[3-(4-chloranylphenoxy)phenyl]pyrrolidin-2-imine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
Resolution 2.64 Å R-free 0.206
8OG8 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 3 Deposited 2023-03-19 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L VM8 5-(2-methyl-1-phenyl-propan-2-yl)imidazo[2,1-a]isoquinoline × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
Resolution 2.11 Å R-free 0.212
8OG9 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 4 Deposited 2023-03-19 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L VM3 5-[1-(4-chlorophenyl)cyclopropyl]imidazo[2,1-a]isoquinoline × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
Resolution 2.94 Å R-free 0.240
8OGA Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 6 Deposited 2023-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain P 1079–1393（315 aa）
Mutation：Q1250L EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 2 VLW 5-[1-(4-methoxyphenyl)cyclopropyl]-8-(4-methylpiperazin-1-yl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 1.66M Lithium acetate
Resolution 2.20 Å R-free 0.209
8OGB Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 8 Deposited 2023-03-19 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L EDO 1,2-ETHANEDIOL × 1 VN5 ~{N}'-[2-[1-(4-methoxyphenyl)cyclopropyl]-7-(4-methylpiperazin-1-yl)quinazolin-4-yl]ethane-1,2-diamine × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 2.13M Lithium acetate
Resolution 2.27 Å R-free 0.212
8OGC Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 11 Deposited 2023-03-19 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L DMS DIMETHYL SULFOXIDE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 VMZ 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]ethanone × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 2.18M Lithium acetate
Resolution 2.09 Å R-free 0.202
8OO5 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 13 Deposited 2023-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain P 1079–1393（315 aa）
Mutation：Q1250L VUF 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclohexyl]quinazolin-7-yl]piperazin-1-yl]ethanone × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.91M LiSO4, 0.1M Tris pH 7.5
Resolution 2.25 Å R-free 0.220
8OOD Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15 Deposited 2023-04-05 Different construct Different mutation/modification 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 1039–1401（363 aa）
Mutation：Q1250L MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 5 VY3 ~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]ethanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.13M LiSO4, 0.1M Tris pH 7.5
Resolution 1.50 Å R-free 0.186
9B9H Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333 Deposited 2024-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1080–1390（311 aa） Fragment：residues 1080-1390
Not recorded A1AM2 N-{(1P)-5'-({(17E)-18-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-16-oxo-3,6,9,12-tetraoxa-15-azaoctadec-17-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；5% w/v 1-ethyl-3-methylimidazolium ethyl sulfate, 15% w/v polyethylene glycol 20,000, pH 7.9
Resolution 2.06 Å R-free 0.229
9B9T Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40407 Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1080–1390（311 aa） Fragment：residues 1080-1390
Not recorded A1ANM N-{(1P)-5'-[(17-{(4P)-4-[(2P)-4-{[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-1H-pyrazol-1-yl}-16-oxo-3,6,9,12-tetraoxa-15-azaheptadecan-1-yl)carbamoyl]-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate trihydrate, pH 4.6, 2.0 M sodium formate
Resolution 2.05 Å R-free 0.196
9B9W Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40792 Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1080–1390（311 aa） Fragment：residues 1080-1390
Not recorded A1ANN (4P)-N-[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(25E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,24-dioxo-5,8,11,14,17,20-hexaoxa-2,23-diazahexacos-25-en-26-yl]-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；35% v/v tacsimate, pH 7.0
Resolution 1.92 Å R-free 0.183
9BA2 Crystal structure of the binary complex of DCAF1 and WDR5 Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1080–1390（311 aa） Fragment：residues 1080-1390
Not recorded IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M imidazole, pH 7.4, 20% w/v polyethylene glycol 4,000
Resolution 2.97 Å R-free 0.266
9BHR Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound Deposited 2024-04-21 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1API (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(2-methoxyethyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate
Resolution 1.62 Å R-free 0.187
9BHR Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound Deposited 2024-04-21 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1API (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(2-methoxyethyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate
Resolution 1.62 Å R-free 0.187
9BHS Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound Deposited 2024-04-21 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1APJ (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide × 1 UNL UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide
Resolution 1.43 Å R-free 0.170
9BHS Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound Deposited 2024-04-21 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1APJ (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide × 1 UNL UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide
Resolution 1.43 Å R-free 0.170
9C1Q Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound Deposited 2024-05-29 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1ATT (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(3-methoxyprop-1-yn-1-yl)-1H-pyrrole-3-carboxamide × 1 UNX UNKNOWN LIGAND × 4 NA SODIUM ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate
Resolution 1.80 Å R-free 0.191
9D4E Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103 Deposited 2024-08-12 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1A1Q (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M di-Ammonium Citrate
Resolution 1.70 Å R-free 0.206
9D4E Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103 Deposited 2024-08-12 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1A1Q (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M di-Ammonium Citrate
Resolution 1.70 Å R-free 0.206
9DLW Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41114 Deposited 2024-09-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1080–1390（311 aa） Fragment：residues 1080-1390
Not recorded A1BAF N-{(1P)-5'-({(32E)-33-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-31-oxo-3,6,9,12,15,18,21,24,27-nonaoxa-30-azatritriacont-32-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；294 K；1.8 M Sodium phosphate monobasic monohydrate, potassium phosphate dibasic / pH 6.9
Resolution 2.07 Å R-free 0.242
9NSN Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41059 Deposited 2025-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1080–1390（311 aa） Fragment：residues 1080-1390
Not recorded A1B0X N-{(1P)-5'-({(26E)-27-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-25-oxo-3,6,9,12,15,18,21-heptaoxa-24-azaheptacos-26-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.15 M cesium chloride, 15% PEG3350
Resolution 1.85 Å R-free 0.234
9NSO Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41060 Deposited 2025-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1080–1390（311 aa） Fragment：residues 1080-1390
Not recorded A1B0Y (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(34E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,33-dioxo-5,8,11,14,17,20,23,26,29-nonaoxa-2,32-diazapentatriacont-34-en-35-yl]-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M sodium citrate tribasic dihydrate, pH 4.2, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic monohydrate
Resolution 1.85 Å R-free 0.218
9PLY Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156 Deposited 2025-07-16 Different construct 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 1077–1390（314 aa）
Chain B 1077–1390（314 aa）
Not recorded A1CI0 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(3-methoxypropyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 2 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M Magnesium formate
Resolution 1.40 Å R-free 0.174
9Y4Q Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102 Deposited 2025-09-03 Different construct 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 1077–1390（314 aa）
Chain B 1077–1390（314 aa）
Not recorded A1CR9 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(pyrimidin-5-yl)-1H-pyrrole-3-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；3.2 M NaCl, 0.1 M Bis-Tris Propane pH 7.0
Resolution 1.48 Å R-free 0.193
9Y76 Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120 Deposited 2025-09-09 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1CSX (4P,5M)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{1-[2-(morpholin-4-yl)ethyl]-1H-pyrazol-4-yl}-1H-pyrrole-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M magnesium formate
Resolution 1.56 Å R-free 0.208
9Y76 Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120 Deposited 2025-09-09 Different construct Different mutation/modification 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 1077–1390（314 aa）
Not recorded A1CSX (4P,5M)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{1-[2-(morpholin-4-yl)ethyl]-1H-pyrazol-4-yl}-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M magnesium formate
Resolution 1.56 Å R-free 0.208
9YDG Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074 Deposited 2025-09-22 Different construct Different mutation/modification 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 1080–1390（311 aa）
Not recorded A1CU7 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M Potassium Fluoride
Resolution 1.54 Å R-free 0.218
9YDG Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074 Deposited 2025-09-22 Different construct Different mutation/modification 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 1080–1390（311 aa）
Not recorded A1CU7 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M Potassium Fluoride
Resolution 1.54 Å R-free 0.218
9YE4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110 Deposited 2025-09-23 Different construct Different mutation/modification 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 1080–1390（311 aa）
Not recorded A1CVQ (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG 3350, 0.1 M Ammonium Sulphate, 0.1 M Bis-Tris pH 5.5
Resolution 1.74 Å R-free 0.224
9YE4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110 Deposited 2025-09-23 Different construct Different mutation/modification 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 1080–1390（311 aa）
Not recorded A1CVQ (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG 3350, 0.1 M Ammonium Sulphate, 0.1 M Bis-Tris pH 5.5
Resolution 1.74 Å R-free 0.224
9YV4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109 Deposited 2025-10-23 Different construct Different mutation/modification 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 1080–1390（311 aa）
Not recorded A1CY9 (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 1 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG 3350, 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5
Resolution 1.60 Å R-free 0.194
9YV4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109 Deposited 2025-10-23 Different construct Different mutation/modification 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 1080–1390（311 aa）
Not recorded A1CY9 (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG 3350, 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5
Resolution 1.60 Å R-free 0.194
9ZL9 Crystal structure of DCAF1 in complex with SDIPTAC C7 Deposited 2025-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1077–1390（314 aa）
Chain B 1077–1390（314 aa）
Chain C 1077–1390（314 aa）
Chain D 1077–1390（314 aa）
Chain E 1077–1390（314 aa）
Chain F 1077–1390（314 aa）
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C23 (4P,4'P)-5,5'-[(1E,30E)-3,29-dioxo-7,10,13,16,19,22,25-heptaoxa-4,28-diazahentriaconta-1,30-diene-1,31-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；294.15 K；0.2 M sodium fluoride, 20% w/v PEG 3350, pH 7.3
Resolution 2.60 Å R-free 0.317
9ZLE Crystal structure of DCAF1 in complex with SDIPTAC C8 Deposited 2025-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1077–1390（314 aa）
Chain B 1077–1390（314 aa）
Chain C 1077–1390（314 aa）
Chain D 1077–1390（314 aa）
Chain E 1077–1390（314 aa）
Chain F 1077–1390（314 aa）
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C25 (4P,4'P)-5,5'-[(1E,33E)-3,32-dioxo-7,10,13,16,19,22,25,28-octaoxa-4,31-diazatetratriaconta-1,33-diene-1,34-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294.15 K；1.0 M ammonium tartrate dibasic, 0.1 M sodium acetate trihydrate, pH 4.6
Resolution 2.55 Å R-free 0.305
9ZLG Crystal structure of DCAF1 in complex with SDIPTAC C9 Deposited 2025-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1077–1390（314 aa）
Chain B 1077–1390（314 aa）
Chain C 1077–1390（314 aa）
Chain D 1077–1390（314 aa）
Chain E 1077–1390（314 aa）
Chain F 1077–1390（314 aa）
Chain G 1077–1390（314 aa）
Chain H 1077–1390（314 aa）
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C26 (4P,4'P)-5,5'-[(1E,36E)-3,35-dioxo-7,10,13,16,19,22,25,28,31-nonaoxa-4,34-diazaheptatriaconta-1,36-diene-1,37-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；5% w/v 1-ethyl-3-methylimidazolium acetate, 15% w/v PEG 20,000, pH 6.5
Resolution 2.30 Å R-free 0.289
9ZLI Crystal structure of DCAF1 in complex with SDIPTAC C11 Deposited 2025-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1077–1390（314 aa）
Chain B 1077–1390（314 aa）
Chain C 1077–1390（314 aa）
Chain D 1077–1390（314 aa）
Chain E 1077–1390（314 aa）
Chain F 1077–1390（314 aa）
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.07 Å R-free 0.278

46 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DCAF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 234–266； UniProt 1475–1507 Author chain B； PDBConstruct 234–266； UniProt 1475–1507

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

SAXS profile for 6n45

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6n45
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6n45
Deposition date deposition_date2018-11-17
Structure title titleCrystal structure of the cryptic polo box domain of human activated Plk4 variant 1
Keywords keywordsPolo-like kinase 4, protein phosphorylation, centriole duplication, PCM organization, phase separation, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.72 Å
Radius of gyration Rg (electron density) rg_electron27.10 Å
Forward intensity I(0) i029501300.00
Molecular weight molecular_weight41407.0 kDa
Excluded volume excluded_volume51471 ų
Envelope volume envelope_volume69305 ų
Hydration-shell volume shell_volume22610 ų
Envelope diameter envelope_diameter93.0 Å
Shell Rg shell_rg32.55 Å
Envelope Rg envelope_rg27.33 Å
Shape Rg shape_rg27.13 Å
Total Rg total_rg27.65 Å
Total atoms total_atoms2933
Residues n_residues407
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax90.0 Å
Rg (real space) rg_real27.83 Å
Rg uncertainty (real space) rg_real_error0.75 Å
I(0) (real space) i0_real2.9500e+07
I(0) uncertainty (real space) i0_real_error4.2290e+05
Rg (reciprocal space) rg_reciprocal27.80 Å
I(0) (reciprocal space) i0_reciprocal29500000.0000
Solution quality estimate total_estimate0.6613
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.9 Å
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.292
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5630000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 0.075; Positv: 1.000; Valcen: 0.925; Smooth: 0.780
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6n45A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily120 —
Domain ID domain_id6n45A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily130 —
Domain ID domain_id6n45B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily120 —
Domain ID domain_id6n45B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily130 —
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8. Citations (1)

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9. Files and Curves (10)