Download MendeleyCrystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4
Zhang, Y.S., Parkinson, G.N., Wei, D.G.To be published.
6KFL
Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4
- PDB DOI: https://doi.org/10.2210/pdb6KFL/pdb
- NAKB: 6KFL
- Classification: DNA
- Organism(s): Pseudorabies virus Ea
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2019-07-08 Released: 2020-07-08
- Funding Organization(s): National Natural Science Foundation of China
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.92 Å
- R-Value Free: 0.262
- R-Value Work: 0.218
- R-Value Observed: 0.221
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 nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*GP*GP*CP*TP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3') | 14 | Pseudorabies virus Ea |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| POH (Subject of Investigation/LOI) Query on POH | G [auth A] | (1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin C44 H38 N8 ABCGFHPGHXSVKI-LWQDQPMZSA-O |  | ||
| NCO (Subject of Investigation/LOI) Query on NCO | H [auth A] | COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N |  | ||
| K (Subject of Investigation/LOI) Query on K | C [auth A], D [auth A], E [auth A], F [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.92 Å
- R-Value Free: 0.262
- R-Value Work: 0.218
- R-Value Observed: 0.221
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.152 | α = 90 |
| b = 47.192 | β = 113.15 |
| c = 38.133 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-07-08 Deposition Author(s): Zhang, Y.S., Parkinson, G.N., Wei, D.G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China | China | 31672558 |
Revision History (Full details and data files)
- Version 1.0: 2020-07-08
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
