DNA TOPOISOMERASE I
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric(3) Consistent with all polymer counts | Chain A; UniProt 203–765 | Fragment:C-TERMINAL DOMAIN, RESIDUES 203-765 Mutation:Y723F | ;DNA (5'-D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3') ; × 1 ;DNA (5'-D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3') ; × 1 | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.8;295 K;27% PEG 400, 145 mM MgCl2, 20 mM MES pH 6.8, 5 mM Tris pH 8.0, 30 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K | Resolution 2.60 Å R-free 0.281 |
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 1EJ9 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1A35 HUMAN TOPOISOMERASE I/DNA COMPLEX Deposited 1998-01-29 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain A
175–765(591 aa)
Fragment:CORE DOMAIN AND C-TERMINAL DOMAIN
|
Mutation:Y723F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.7;295 K;pH 7.70, VAPOR DIFFUSION, SITTING DROP, temperature 295.00K
|
Resolution 2.50 Å R-free 0.308 |
| 1A36 TOPOISOMERASE I/DNA COMPLEX Deposited 1998-01-29 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain A
174–765(592 aa)
Fragment:CORE DOMAIN AND C-TERMINAL DOMAIN
|
Mutation:Y723F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.7;pH 7.70
|
Resolution 2.80 Å R-free 0.312 |
| 1K4S HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX Deposited 2001-10-08 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric |
Chain A
174–765(592 aa)
Fragment:Core Domain and C-Terminal Domain, Residues 174-765
|
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, SITTING DROP;pH 8;289 K;PEG 8000, Tris-HCl, Na/K Phosphate, KCl, DTT, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 3.20 Å R-free 0.222 |
| 1K4T HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX Deposited 2001-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric |
Chain A
174–765(592 aa)
Fragment:Core Domain and C-Terminal Domain, Residues 174-765
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | TTG 2-(1-DIMETHYLAMINOMETHYL-2-HYDROXY-8-HYDROXYMETHYL-9-OXO-9,11-DIHYDRO-INDOLIZINO[1,2-B]QUINOLIN-7-YL)-2-HYDROXY-BUTYRIC ACID × 1 TTC (S)-10-[(DIMETHYLAMINO)METHYL]-4-ETHYL-4,9-DIHYDROXY-1H-PYRANO[3',4':6,7]INOLIZINO[1,2-B]-QUINOLINE-3,14(4H,12H)-DIONE × 1 HG MERCURY (II) ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.5;289 K;PEG 8000, Ammonium Sulfate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 2.10 Å R-free 0.269 |
| 1LPQ Human DNA Topoisomerase I (70 Kda) In Non-Covalent Complex With A 22 Base Pair DNA Duplex Containing an 8-oxoG Lesion Deposited 2002-05-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain A
202–765(564 aa)
|
Mutation:Y723F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.8;295 K;Tris-HCl, MES, PEG 400, Magnesium chloride, dithiothreitol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.14 Å R-free 0.298 |
| 1NH3 Human Topoisomerase I Ara-C Complex Deposited 2002-12-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric |
Chain A
203–764(562 aa)
Fragment:Core Subdomain, C-Terminal Domain
|
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, SITTING DROP;pH 7.7;276 K;Tris, Magnesium Chloride, PEG 400, DTT, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 276K
|
Resolution 3.10 Å R-free 0.311 |
| 1R49 Human topoisomerase I (Topo70) double mutant K532R/Y723F Deposited 2003-10-03 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain A
174–765(592 aa)
Fragment:Topo70
|
Mutation:K532R, Y723F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 7.5;298 K;PEG 3350 MME, Magnesium chloride, MES, TCEP, pH 7.5, VAPOR DIFFUSION, temperature 298K
|
Resolution 3.13 Å R-free 0.339 |
| 1RR8 Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I Deposited 2003-12-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain C
203–765(563 aa)
|
Mutation:F361S,Q634R Non-standard monomer:Yes (specific site not provided by mmCIF) | TTG 2-(1-DIMETHYLAMINOMETHYL-2-HYDROXY-8-HYDROXYMETHYL-9-OXO-9,11-DIHYDRO-INDOLIZINO[1,2-B]QUINOLIN-7-YL)-2-HYDROXY-BUTYRIC ACID × 1 TTC (S)-10-[(DIMETHYLAMINO)METHYL]-4-ETHYL-4,9-DIHYDROXY-1H-PYRANO[3',4':6,7]INOLIZINO[1,2-B]-QUINOLINE-3,14(4H,12H)-DIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;PEG 8000, 200mM Lithium Sulfate, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.60 Å R-free 0.294 |
| 1RRJ Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I Deposited 2003-12-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain A
201–765(565 aa)
|
Mutation:Asn722Ser Non-standard monomer:Yes (specific site not provided by mmCIF) | TTG 2-(1-DIMETHYLAMINOMETHYL-2-HYDROXY-8-HYDROXYMETHYL-9-OXO-9,11-DIHYDRO-INDOLIZINO[1,2-B]QUINOLIN-7-YL)-2-HYDROXY-BUTYRIC ACID × 1 TTC (S)-10-[(DIMETHYLAMINO)METHYL]-4-ETHYL-4,9-DIHYDROXY-1H-PYRANO[3',4':6,7]INOLIZINO[1,2-B]-QUINOLINE-3,14(4H,12H)-DIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;PEG8000, 200mM lithium sulfate, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.30 Å R-free 0.278 |
| 1SC7 Human DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoquinoline MJ-II-38 and Covalent Complex With A 22 Base Pair DNA Duplex Deposited 2004-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric |
Chain A
174–765(592 aa)
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | M38 4-(5,11-DIOXO-5H-INDENO[1,2-C]ISOQUINOLIN-6(11H)-YL)BUTANOATE × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.4;289 K;PEG 8000, AMMONIUM SULFATE, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 3.00 Å R-free 0.285 |
| 1SEU Human DNA Topoisomerase I (70 Kda) In Complex With The Indolocarbazole SA315F and Covalent Complex With A 22 Base Pair DNA Duplex Deposited 2004-02-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric |
Chain A
174–765(592 aa)
|
Mutation:Asn722Ser Non-standard monomer:Yes (specific site not provided by mmCIF) | SA3 2,10-DIHYDROXY-12-(BETA-D-GLUCOPYRANOSYL)-6,7,12,13-TETRAHYDROINDOLO[2,3-A]PYRROLO[3,4-C]CARBAZOLE-5,7-DIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.4;289 K;PEG 8000, AMMONIUM SULFATE, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 3.00 Å R-free 0.295 |
| 1T8I Human DNA Topoisomerase I (70 Kda) In Complex With The Poison Camptothecin and Covalent Complex With A 22 Base Pair DNA Duplex Deposited 2004-05-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric |
Chain A
174–765(592 aa)
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | EHD 4-ETHYL-4-HYDROXY-1,12-DIHYDRO-4H-2-OXA-6,12A-DIAZA-DIBENZO[B,H]FLUORENE-3,13-DIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.4;289 K;PEG 8000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 3.00 Å R-free 0.292 |
| 1TL8 Human DNA topoisomerase I (70 kDa) in complex with the indenoisoquinoline AI-III-52 and covalent complex with a 22 base pair DNA duplex Deposited 2004-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: tetrameric |
Chain A
174–765(592 aa)
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | AI3 2,3-DIMETHOXY-12H-[1,3]DIOXOLO[5,6]INDENO[1,2-C]ISOQUINOLIN-6-IUM × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.4;289 K;PEG 8000, MES, Ammonium Sulfate, pH 6.40, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 3.10 Å R-free 0.305 |
13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | TOP1_HUMAN |
| Isoform | — |
| PDB entities | 3 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–563; UniProt 203–765 |