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.
5HRL
The crystal structure of AsfvPolX: 1nt-gap(P) DNA2: dGTP ternary complex.
- PDB DOI: https://doi.org/10.2210/pdb5HRL/pdb
- NAKB: 5HRL
- 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: 2.40 Å
- R-Value Free: 0.257
- R-Value Work: 0.228
- R-Value Observed: 0.229
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 beta-like protein | A, E [auth B] | 178 | African swine fever virus | Mutation(s): 0 Gene Names: O174L EC: 2.7.7.7 |  |
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 | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3') | B [auth C], F | 18 | synthetic construct |  | |
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*TP*GP*AP*GP*TP*AP*CP*A)-3') | C [auth D], G | 9 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3') | D [auth E], H | 8 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DGT Query on DGT | I [auth A], M [auth B] | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N |  | ||
| GOL Query on GOL | L [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MN Query on MN | J [auth A], K [auth A], N [auth B], O [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.257
- R-Value Work: 0.228
- R-Value Observed: 0.229
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 124.651 | α = 90 |
| b = 71.348 | β = 90 |
| c = 86.922 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | 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: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
