Download MendeleyStructural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus
Zhang, Y.S., Parkinson, G.N., Wei, D.G.To be published.
6XRQ
Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus
- PDB DOI: https://doi.org/10.2210/pdb6XRQ/pdb
- NAKB: 6XRQ
- Classification: RNA
- Organism(s): Pseudorabies virus Ea
- Mutation(s): No
- Deposited: 2020-07-13 Released: 2021-07-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.21 Å
- R-Value Free: 0.217
- R-Value Work: 0.199
- R-Value Observed: 0.200
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| RNA (5' GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A-3') | A [auth B], B [auth A] | 14 | Pseudorabies virus Ea |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| V8A (Subject of Investigation/LOI) Query on V8A | F [auth A], G [auth A] | 2,7-bis[3-(morpholin-4-yl)propyl]-4,9-bis{[3-(morpholin-4-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone C42 H60 N8 O8 PBXBULWQEKJFOX-UHFFFAOYSA-N |  | ||
| K Query on K | C [auth B], D [auth B], E [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.21 Å
- R-Value Free: 0.217
- R-Value Work: 0.199
- R-Value Observed: 0.200
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 29.177 | α = 90 |
| b = 43.974 | β = 108.39 |
| c = 30.781 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2021-07-28 Deposition Author(s): Zhang, Y.S., Parkinson, G.N., Wei, D.G.
Revision History (Full details and data files)
- Version 1.0: 2021-07-28
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Database references, Derived calculations, Refinement description
