Download MendeleyA Y-family polymerase complexed with abasic lesions: catching DNA with a loaded nucleoside triphosphate
Ling, H., Boudsocq, F., Woodgate, R., Yang, W.To be published.
1N48
Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion
- PDB DOI: https://doi.org/10.2210/pdb1N48/pdb
- NAKB: 1N48
- Classification: TRANSFERASE/DNA
- Organism(s): Saccharolobus solfataricus P2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2002-10-30 Released: 2004-02-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 ?
- R-Value Free: 0.230
- R-Value Work: 0.204
- R-Value Observed: 0.204
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase IV | C [auth A] | 352 | Saccharolobus solfataricus P2 | Mutation(s): 0 Gene Names: dpo4 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 | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' | A [auth B] | 13 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*CP*AP*(3DR)P*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | B [auth C] | 16 | N/A |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | E [auth B] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| CA Query on CA | D [auth B], F [auth A], G [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 ?
- R-Value Free: 0.230
- R-Value Work: 0.204
- R-Value Observed: 0.204
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 75.546 | ¦Á = 90 |
| b = 88.458 | ¦Â = 90 |
| c = 92.389 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
Entry History
Deposition Data
- Released Date: 2004-02-24 Deposition Author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.
Revision History (Full details and data files)
- Version 1.0: 2004-02-24
Type: Initial release - Version 1.1: 2008-04-28
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
