Download MendeleyStructure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
Koag, M.-C., Lee, S.To be published.
7KLF
Ternary structure of Dpo4 bound to G in the template base paired with incoming dCTP
- PDB DOI: https://doi.org/10.2210/pdb7KLF/pdb
- NAKB: 7KLF
- Classification: DNA BINDING PROTEIN
- Organism(s): Saccharolobus solfataricus P2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2020-10-30 Released: 2021-11-03
- Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.279
- R-Value Work: 0.231
- R-Value Observed: 0.234
Starting Model: experimental
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This is version 1.1 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*AP*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 | |
| DCP (Subject of Investigation/LOI) Query on DCP | G [auth A] | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-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: 2.30 Å
- R-Value Free: 0.279
- R-Value Work: 0.231
- R-Value Observed: 0.234
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.52 | α = 90 |
| b = 102.373 | β = 90 |
| c = 52.959 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-11-03 Deposition Author(s): Koag, M.-C., Lee, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) | United States | ES-26676 |
Revision History (Full details and data files)
- Version 1.0: 2021-11-03
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
