9FTA | pdb_00009fta

Crystal structure of d(GGGGTTTTGGGG) with Zn and K

PDB DOI: https://doi.org/10.2210/pdb9FTA/pdb
NAKB: 9FTA

Classification: DNA
Organism(s): DNA molecule
Mutation(s): No

Deposited: 2024-06-24 Released: 2025-07-02
Deposition Author(s): Sbirkova-Dimitrova, H.I., Shivachev, B.L.
Funding Organization(s): Bulgarian National Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.426 (Depositor), 0.433 (DCC)
R-Value Work:
0.334 (Depositor), 0.338 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of d(GGGGTTTTGGGG) with Zn and K

Sbirkova-Dimitrova, H.I., Shivachev, B.L.

To be published.

Macromolecule Content

Total Structure Weight: 15.98 kDa
Atom Count: 1,070
Modeled Residue Count: 48
Deposited Residue Count: 48
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(GPGPGPGPTPTPTPTPGPGPGPG)-3')	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	12	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain T [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain T [auth DDD] mmCIF format, chain K [auth AAA] mmCIF format, chain M [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain T [auth DDD]	K [auth AAA], M [auth BBB], N [auth BBB], T [auth DDD]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain T [auth DDD]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain L [auth BBB] SDF format, chain O [auth CCC] SDF format, chain P [auth CCC] SDF format, chain Q [auth CCC] SDF format, chain R [auth CCC] SDF format, chain S [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain O [auth CCC] MOL2 format, chain P [auth CCC] MOL2 format, chain Q [auth CCC] MOL2 format, chain R [auth CCC] MOL2 format, chain S [auth CCC] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain O [auth CCC] mmCIF format, chain P [auth CCC] mmCIF format, chain Q [auth CCC] mmCIF format, chain R [auth CCC] mmCIF format, chain S [auth CCC]	E [auth AAA] F [auth AAA] G [auth AAA] H [auth AAA] I [auth AAA] E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], L [auth BBB], O [auth CCC], P [auth CCC], Q [auth CCC], R [auth CCC], S [auth CCC]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain L [auth BBB] Focus chain O [auth CCC] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain R [auth CCC] Focus chain S [auth CCC]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain U [auth DDD] MOL2 format, chain U [auth DDD] mmCIF format, chain U [auth DDD]	U [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain U [auth DDD]