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Crystallization of the tl+-form of the oxytricha nova G-quadruplex

Analyse Crystallization of the tl+-form of the oxytricha nova G-quadruplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HBN
Type: DNA
Length: 48 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
Ligands: TL
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	5'-D(GPGPGPGPTPTPTPTPGPGPGPG)-3'	dna	12	—	—

Ligands and binding sites

TL · Thallium (I) 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	180	0.58	0.82	19	TL

Interfaces

5 interfaces between chains.

A–B · 815 Å² buried · 62 hydrogen bonds · nucleic-nucleic
C–D · 814 Å² buried · 60 hydrogen bonds · nucleic-nucleic
A–C · 145 Å² buried · 4 hydrogen bonds · nucleic-nucleic
A–D · 41 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–C · 40 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

2HBN · Crystallization of the Tl+-form of the Oxytricha nova 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 2HBN · PDBe 2HBN

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