Download MendeleyStructure of E. coli Topoisomerase I Trapped as Covalent Complex Intermediate with Cleaved DNA
Tse-Dinh, Y.C., Zhang, Z., Cheng, B.To be published.
3PX7
Crystal Structure of covalent complex of topoisomerase 1A with substrate
- PDB DOI: https://doi.org/10.2210/pdb3PX7/pdb
- NAKB: 3PX7
- Classification: ISOMERASE/DNA
- Organism(s): Escherichia coli DH1
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2010-12-09 Released: 2011-04-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.269
- R-Value Work: 0.230
- R-Value Observed: 0.230
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA topoisomerase | 595 | Escherichia coli DH1 | Mutation(s): 1 Gene Names: 415337, EcDH1_2375 EC: 5.99.1.2 |  | |
UniProt | |||||
Find proteins for P06612 (Escherichia coli (strain K12)) Explore P06612 Go to UniProtKB: P06612 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06612 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA 5'-D(*TP*TP*GP*GP*G)-3' | 5 | N/A |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HG Query on HG | D [auth A], E [auth B], F [auth C] | MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PTR Query on PTR | A | L-PEPTIDE LINKING | C9 H12 N O6 P |  | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.269
- R-Value Work: 0.230
- R-Value Observed: 0.230
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 61.602 | α = 90 |
| b = 91.759 | β = 90 |
| c = 141.976 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| HKL-3000 | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2011-04-20 Deposition Author(s): Zhang, Z., Tse-dinh, Y.C., Cheng, B.
Revision History (Full details and data files)
- Version 1.0: 2011-04-20
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description
