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Crystal structure of the 2'- deoxyguanosine riboswitch bound to guanosine

Analyse Crystal structure of the 2'- deoxyguanosine riboswitch bound to guanosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SKZ
Type: RNA
Length: 136 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (68-mer)
Ligands: GMP, MG, SO4
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (68-mer)	rna	68	—	—

Ligands and binding sites

GMP · Guanosine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B
SIN · Succinic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1043	0.75	0.79	57	GMP, MG, SO4
2	762	0.72	0.79	45	GMP, MG, SO4
3	482	0.57	0.74	23	SO4

Interfaces

1 interface between chains.

A–B · 400 Å² buried · 25 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

3SKZ · Crystal structure of the 2'- deoxyguanosine riboswitch bound to guanosine · the same entry in another collection · chain B against B, 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 3SKZ · PDBe 3SKZ

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