Download MendeleyThe crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1
Chen, Y.Q., Zhang, J., Gan, J.H.To be published.
5HRF
The crystal structure of AsfvPolX: DNA5: dGTP ternary complex
- PDB DOI: https://doi.org/10.2210/pdb5HRF/pdb
- NAKB: 5HRF
- Classification: TRANSFERASE/DNA
- Organism(s): African swine fever virus, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-01-23 Released: 2017-01-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.263
- R-Value Work: 0.212
- R-Value Observed: 0.215
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 beta-like protein | 178 | African swine fever virus | Mutation(s): 0 Gene Names: O174L |  | |
UniProt | |||||
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore P42494 Go to UniProtKB: P42494 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P42494 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-3') | 9 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DGT Query on DGT | F [auth A], I [auth B] | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N |  | ||
| SO4 Query on SO4 | H [auth B], J [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| MN Query on MN | E [auth A], G [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.263
- R-Value Work: 0.212
- R-Value Observed: 0.215
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.706 | α = 90 |
| b = 75.441 | β = 90 |
| c = 108.45 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-01-18 Deposition Author(s): Chen, Y.Q., Zhang, J., Gan, J.H.
Revision History (Full details and data files)
- Version 1.0: 2017-01-18
Type: Initial release - Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations, Refinement description
