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The structure of the thermobifida fusca guanidine III riboswitch in space group P212121.

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PDB: 5NZD
Type: RNA
Length: 82 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanidine III riboswitch
Ligands: MG, NA
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Guanidine III riboswitch	rna	41	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 9 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A
ACT · Acetate ion · additive · 2 copies · chains A, B

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	152	0.55	0.82	12	MG, ACT
2	127	0.49	0.80	11	MG, ACT
3	69	0.29	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 81 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

5NZD · The structure of the thermobifida fusca guanidine III riboswitch in space group P212121. · 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 5NZD · PDBe 5NZD

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