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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：P0ABS5 New Search
11PDB entries
21Biological assembly
25chain/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
1DD9 STRUCTURE OF THE DNAG CATALYTIC CORE Deposited 1999-11-09 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 111–433（323 aa） Fragment：36 KDA CATALYTIC CORE DOMAIN
Not recorded SR STRONTIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM SRCL2, VAPOR DIFFUSION, HANGING DROP
Resolution 1.60 Å R-free 0.276
1DDE STRUCTURE OF THE DNAG CATALYTIC CORE Deposited 1999-11-09 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 111–433（323 aa） Fragment：36 KDA CATALYTIC CORE DOMAIN
Not recorded Y1 YTTRIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM YCL2, VAPOR DIFFUSION, HANGING DROP
Resolution 1.70 Å R-free 0.263
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 109–429（321 aa） Fragment：CATALYTIC CORE
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 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 109–429（321 aa） Fragment：CATALYTIC CORE
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 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 109–429（321 aa） Fragment：CATALYTIC CORE
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 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 109–429（321 aa） Fragment：CATALYTIC CORE
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 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain E 109–429（321 aa） Fragment：CATALYTIC CORE
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 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 434–581（148 aa）
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 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 434–581（148 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28 Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 434–581（148 aa）
Chain B 434–581（148 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
2HAJ Solution structure of the helicase-binding domain of Escherichia coli primase Deposited 2006-06-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 434–581（148 aa） Fragment：Helicase-binding domain, residues 447-581
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR sample composition 0.3mM DnaG-C U-15N, 13C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3mM DnaG-C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3B39 Structure of the DnaG primase catalytic domain bound to ssDNA Deposited 2007-10-19 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain A 111–429（319 aa） Fragment：RNA Polymerase Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.35 Å R-free 0.254
3B39 Structure of the DnaG primase catalytic domain bound to ssDNA Deposited 2007-10-19 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain B 111–429（319 aa） Fragment：RNA Polymerase Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.35 Å R-free 0.254
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6
Resolution 1.50 Å R-free 0.179
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6
Resolution 1.50 Å R-free 0.179
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 3 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 1.85 Å R-free 0.224
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 3 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 1.85 Å R-free 0.224
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 2.10 Å R-free 0.229
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 2.10 Å R-free 0.229
7T22 E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2021-12-02 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: decameric（10） Consistent with all polymers
Chain G 434–581（148 aa） Fragment：C-terminal domain
Chain H 434–581（148 aa） Fragment：C-terminal domain
Chain I 434–581（148 aa） Fragment：C-terminal domain
Mutation：R568C Mutation：R568C Mutation：R568C ADP ADENOSINE-5'-DIPHOSPHATE × 5 ALF TETRAFLUOROALUMINATE ION × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP.
cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.
Resolution 4.20 Å
9ECO E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2024-11-14 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain G 434–581（148 aa） Fragment：C-terminal domain
Chain H 434–581（148 aa） Fragment：C-terminal domain
Mutation：R568C Mutation：R568C ALF TETRAFLUOROALUMINATE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP, 0.5 mM AlCl3, 5 mM NaF.
cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.
Resolution 2.83 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.