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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：P06612 New Search
20PDB entries
22Biological assembly
26chain/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
1CY0 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-5'-ADENOSINE DIPHOSPHATE Deposited 1999-08-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Not recorded A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 5；287 K；2.14M ammonium sulfate, pH 5.0, MICRODIALYSIS, temperature 287K
Resolution 2.45 Å R-free 0.274
1CY1 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'PTPTPT Deposited 1999-08-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Not recorded PO4 PHOSPHATE ION × 1 TMP THYMIDINE-5'-PHOSPHATE × 2 THP THYMIDINE-3',5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.3M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 2.30 Å R-free 0.307
1CY2 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH TPTPTP3' Deposited 1999-08-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Not recorded PO4 PHOSPHATE ION × 1 TMP THYMIDINE-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.3M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 2.30 Å R-free 0.284
1CY4 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3' Deposited 1999-08-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Not recorded PO4 PHOSPHATE ION × 3 TMP THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.55 Å R-free 0.299
1CY6 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3' THYMIDINE MONOPHOSPHATE Deposited 1999-08-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Not recorded PO4 PHOSPHATE ION × 3 T3P THYMIDINE-3'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 2.50 Å R-free 0.309
1CY7 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE Deposited 1999-08-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Mutation：GLY-SER ATTACHED AT N-TERMINUS DUE TO CONSTRUCT PO4 PHOSPHATE ION × 1 TMP THYMIDINE-5'-PHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；2.3M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.295
1CY8 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'-THYMIDINE MONOPHOSPHATE Deposited 1999-08-31 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Not recorded PO4 PHOSPHATE ION × 1 T3P THYMIDINE-3'-PHOSPHATE × 1 TMP THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 2.45 Å R-free 0.295
1CY9 CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM Deposited 1999-08-31 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；11-13%(W/V) PEG 3500, 20MM MES PH 6.0, 50MM KCL, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.242
1CYY CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM Deposited 1999-08-31 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.15 Å R-free 0.282
1CYY CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM Deposited 1999-08-31 Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.15 Å R-free 0.282
1CYY CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM Deposited 1999-08-31 Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.15 Å R-free 0.282
1ECL AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1). Deposited 1995-05-05 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–597（597 aa）
Mutation：GLY SER INSERTION AT N-TERMINUS, INSERTION OF STOP CODON AT 598; ENGINEERED No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1MW8 Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3' Deposited 2002-09-27 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain X 1–592（592 aa） Fragment：67 kDa N-terminal fragment
Mutation：H365R SO4 SULFATE ION × 5 TMP THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；ammonium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 1.90 Å R-free 0.273
1MW9 Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I Deposited 2002-09-27 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain X 1–592（592 aa） Fragment：67 kDa N-terminal fragment
Mutation：H365R SO4 SULFATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions DIALYSIS；pH 8；287 K；ammonium sulfate, pH 8, DIALYSIS, temperature 287K
Resolution 1.67 Å R-free 0.216
1YUA C-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I Deposited 1995-03-02 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 745–865（121 aa） Fragment：122 C-TERMINAL RESIDUES
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
3PWT Crystal structure of mutant E.coli topoisomerase IA Deposited 2010-12-08 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–596（596 aa） Fragment：N-terminal catalytical domain, 67K
Mutation：D111N SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；288 K；2M ammonium sulfate, pH 7.4, VAPOR DIFFUSION, temperature 288K
Resolution 1.90 Å R-free 0.249
9GDA RNAP-TopoI complex on duplex scaffold Deposited 2024-08-05 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain F 1–865（865 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9GDB RNAP-TopoI complex on bubble scaffold - consensus reconstruction Deposited 2024-08-05 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain F 1–865（865 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GDC RNAP-TopoI complex on bubble scaffold - single-bubble configuration Deposited 2024-08-05 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain F 1–865（865 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9GDD RNAP-TopoI complex on bubble scaffold - two-bubble configuration Deposited 2024-08-05 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain F 1–865（865 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9GDE RNAP-TopoI complex on long-overhang scaffold - orientation 1 Deposited 2024-08-05 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain F 1–865（865 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9GDH RNAP-TopoI complex on long-overhang scaffold - orientation 2 Deposited 2024-08-05 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain F 1–865（865 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 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.