2N9Q | pdb_00002n9q

Photoswitchable G-quadruplex

PDB DOI: https://doi.org/10.2210/pdb2N9Q/pdb
NAKB: 2N9Q
BMRB: 25915

Classification: DNA
Mutation(s): No

Deposited: 2015-12-02 Released: 2016-02-17
Deposition Author(s): Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.P.N., Slavov, C., Jonker, H.R.A., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif.

Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.P., Slavov, C., Jonker, H.R., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.

(2016) Angew Chem Int Ed Engl 55: 2738-2742

PubMed: 26805928 Search on PubMed
DOI: https://doi.org/10.1002/anie.201510269
Primary Citation of Related Structures:
2N9Q

PubMed Abstract:
The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+) ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization.

Organizational Affiliation

Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.

Macromolecule Content

Total Structure Weight: 6.42 kDa
Atom Count: 427
Modelled Residue Count: 20
Deposited Residue Count: 20
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPGP(AZW)PGP*G)-3')	A, B, C, D	5	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth C]	E [auth A], F [auth A], G [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release
Version 1.1: 2016-03-02
Changes: Database references
Version 1.2: 2023-06-14
Changes: Data collection, Database references, Derived calculations, Other
Version 1.3: 2024-05-15
Changes: Data collection, Database references