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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P32325 New Search
10PDB entries
30Biological assembly
32chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain J 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain E 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain F 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain G 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain H 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ0 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain I 120–250（131 aa） Fragment：residues 120-250
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.244
3OQ4 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 120–250（131 aa） Fragment：residues 120-250
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；277 K；22% MPD (v/v) and 100 mM Na/K phosphate buffer pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.229
3OQ4 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 120–250（131 aa） Fragment：residues 120-250
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；277 K；22% MPD (v/v) and 100 mM Na/K phosphate buffer pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.229
3OQ4 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 120–250（131 aa） Fragment：residues 120-250
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；277 K；22% MPD (v/v) and 100 mM Na/K phosphate buffer pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.229
3OQ4 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 120–250（131 aa） Fragment：residues 120-250
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；277 K；22% MPD (v/v) and 100 mM Na/K phosphate buffer pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.229
3OQ4 Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 Deposited 2010-09-02 Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain E 120–250（131 aa） Fragment：residues 120-250
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；277 K；22% MPD (v/v) and 100 mM Na/K phosphate buffer pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.229
3QBZ Crystal structure of the Rad53-recognition domain of Saccharomyces cerevisiae Dbf4 Deposited 2011-01-14 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 66–221（156 aa） Fragment：residues 66-221, HBRCT domain
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.9 M ammonium sulfate 50 mM sodium cacodylate 15 mM CYMAL-7, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.69 Å R-free 0.273
3QBZ Crystal structure of the Rad53-recognition domain of Saccharomyces cerevisiae Dbf4 Deposited 2011-01-14 Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 66–221（156 aa） Fragment：residues 66-221, HBRCT domain
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.9 M ammonium sulfate 50 mM sodium cacodylate 15 mM CYMAL-7, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.69 Å R-free 0.273
5T2F Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4 Deposited 2016-08-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-161 via LINKER residues: VDSGASGGS
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；50 mM sodium cacodylate pH 6.5 12% PEG 4000 (v/v) 250 mM MgCl2
Resolution 2.66 Å R-free 0.237
5T2F Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4 Deposited 2016-08-23 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-161 via LINKER residues: VDSGASGGS
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；50 mM sodium cacodylate pH 6.5 12% PEG 4000 (v/v) 250 mM MgCl2
Resolution 2.66 Å R-free 0.237
5T2F Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4 Deposited 2016-08-23 Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-161 via LINKER residues: VDSGASGGS
Not recorded EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；50 mM sodium cacodylate pH 6.5 12% PEG 4000 (v/v) 250 mM MgCl2
Resolution 2.66 Å R-free 0.237
5T2F Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4 Deposited 2016-08-23 Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-161 via LINKER residues: VDSGASGGS
Not recorded EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；50 mM sodium cacodylate pH 6.5 12% PEG 4000 (v/v) 250 mM MgCl2
Resolution 2.66 Å R-free 0.237
5T2S Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide. Deposited 2016-08-24 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-162 via LINKER residues VDGS
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM TRIS pH 8.5 12.5 % PEG 3350 (v/v)
Resolution 2.40 Å R-free 0.229
5T2S Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide. Deposited 2016-08-24 Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-162 via LINKER residues VDGS
Not recorded GOL GLYCEROL × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM TRIS pH 8.5 12.5 % PEG 3350 (v/v)
Resolution 2.40 Å R-free 0.229
5T2S Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide. Deposited 2016-08-24 Assembly 3 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-162 via LINKER residues VDGS
Chain C 105–220（116 aa） Fragment：UNP P32325 residues 105-220 linked to UNP P22216 residues 22-162 via LINKER residues VDGS
Not recorded GOL GLYCEROL × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM TRIS pH 8.5 12.5 % PEG 3350 (v/v)
Resolution 2.40 Å R-free 0.229
6MF6 Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region. Deposited 2018-09-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 76–96（21 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium potassium tartrate, 10 mM trimethylamine hydrochloride, 20 % PEG 3350.
Resolution 3.40 Å R-free 0.283
6MF6 Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region. Deposited 2018-09-09 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 76–96（21 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium potassium tartrate, 10 mM trimethylamine hydrochloride, 20 % PEG 3350.
Resolution 3.40 Å R-free 0.283
7P5Z Structure of a DNA-loaded MCM double hexamer engaged with the Dbf4-dependent kinase Deposited 2021-07-15 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain G 1–704（704 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 10 ZN ZINC ION × 11 ADP ADENOSINE-5'-DIPHOSPHATE × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 seconds before plunging
Resolution 3.30 Å
7PT6 Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III Deposited 2021-09-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count
Chain 9 1–704（704 aa）
Chain I 1–704（704 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 14 ZN ZINC ION × 14 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1.5 seconds and blot force +2
Resolution 3.20 Å
7PT7 Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I Deposited 2021-09-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
Chain 9 1–704（704 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 13 MG MAGNESIUM ION × 14 ZN ZINC ION × 12 BEF BERYLLIUM TRIFLUORIDE ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1.5 seconds and blot force +2
Resolution 3.80 Å
7V3V Cryo-EM structure of MCM double hexamer bound with DDK in State I Deposited 2021-08-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein count
Chain I 1–704（704 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 12 ZN ZINC ION × 11 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.