MolNFT v1 · #149214 · DNA

Structure of a quadruplex forming sequence from D. discoideum

6FTU · DNA (26-mer): “Structure of a quadruplex forming sequence from D. discoideum”. X-ray diffraction, 1 ligand (K), 3 pockets (best druggability 0.65). MolNFT v1 #149214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FTU
Type: DNA
Length: 175 nucleotides
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (26-mer)
Ligands: K
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, F	DNA (26-mer)	dna	26	—	—
B	DNA (26-mer)	dna	25	—	—
D	DNA (26-mer)	dna	24	—	—
Z	DNA (26-mer)	dna	22	—	—

Ligands and binding sites

K · Potassium ion · metal · 21 copies · chains A, B, C, D, E, F, Z

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	702	0.65	0.75	46	empty
2	111	0.39	0.76	12	empty
3	54	0.23	0.72	10	empty

Interfaces

5 interfaces between chains.

A–C · 362 Å² buried · 3 hydrogen bonds · nucleic-nucleic
C–D · 213 Å² buried · 5 hydrogen bonds · nucleic-nucleic
E–F · 208 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–B · 183 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–E · 32 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

6FTU · Structure of a Quadruplex forming sequence from D. discoideum · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6FTU · PDBe 6FTU

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