Download MendeleyStructure of Dpo4 DNA polymerase replicating across the genotoxic N7-methylguanine lesion
Koag, M.-C., Lee, S.To be published.
5EDW
Ternary structure of Dpo4 bound to G in the template base paired with incoming dTTP
- PDB DOI: https://doi.org/10.2210/pdb5EDW/pdb
- NAKB: 5EDW
- Classification: transferase/dna
- Organism(s): Saccharolobus solfataricus P2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-10-22 Released: 2016-11-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.284
- R-Value Work: 0.220
- R-Value Observed: 0.223
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 polymerase IV | 341 | Saccharolobus solfataricus P2 | Mutation(s): 0 Gene Names: dbh, dpo4, SSO2448 EC: 2.7.7.7 |  | |
UniProt | |||||
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W02 Go to UniProtKB: Q97W02 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q97W02 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | B [auth T] | 19 | Saccharolobus solfataricus P2 |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') | C [auth P] | 13 | Saccharolobus solfataricus P2 |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TTP Query on TTP | G [auth A] | THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N |  | ||
| CA Query on CA | D [auth A], E [auth A], F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.284
- R-Value Work: 0.220
- R-Value Observed: 0.223
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.516 | α = 90 |
| b = 101.994 | β = 90 |
| c = 52.864 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| DENZO | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2016-11-02 Deposition Author(s): Koag, M.-C., Lee, S.
Revision History (Full details and data files)
- Version 1.0: 2016-11-02
Type: Initial release - Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description - Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
