Research workbench

DNA containing both right- and left-handed parallel-stranded G- quadruplexes

Analyse DNA containing both right- and left-handed parallel-stranded G- quadruplexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QJO
Type: DNA
Length: 112 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (28-mer)
Ligands: K
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (28-mer)	dna	28	—	—

Ligands and binding sites

K · Potassium ion · metal · 15 copies · chains A, B, C, D

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	465	0.64	0.78	36	empty
2	268	0.60	0.80	23	K
3	188	0.44	0.75	19	K

Interfaces

4 interfaces between chains.

A–B · 294 Å² buried · 9 hydrogen bonds · nucleic-nucleic
C–D · 283 Å² buried · 10 hydrogen bonds · nucleic-nucleic
A–D · 104 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–C · 12 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

6QJO · DNA containing both right- and left-handed parallel-stranded G-quadruplexes · 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 6QJO · PDBe 6QJO

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