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Crystal structure of a dimeric interlocked parallel G-quadruplex

Analyse Crystal structure of a dimeric interlocked parallel G-quadruplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7XDH
Type: DNA
Length: 63 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.83
Molecule: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3')
Ligands: K
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · resolution 1.83 · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	DNA (5'-D(GPGPGPGPTPGPGPGPAPGPGPAPGPGPGPT)-3')	dna	16	—	—
C	DNA (5'-D(GPGPGPGPTPGPGPGPAPGPGPAPGPGPGPT)-3')	dna	15	—	—

Ligands and binding sites

K · Potassium ion · metal · 10 copies · chains A, B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.46	0.75	17	empty

Interfaces

2 interfaces between chains.

C–D · 557 Å² buried · 24 hydrogen bonds · nucleic-nucleic
A–B · 557 Å² buried · 23 hydrogen bonds · nucleic-nucleic

Compared structures

7XDH · Crystal structure of a dimeric interlocked parallel G-quadruplex · 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 7XDH · PDBe 7XDH

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