MolNFT v1 · #128716 · RNA

The structure of the thermobifida fusca guanidine III riboswitch with methylguanidine

5NZ3 · RNA (41-mer): “The structure of the thermobifida fusca guanidine III riboswitch with methylguanidine”. X-ray diffraction, 3 ligands (MGX, MG, NA), 5 pockets (best druggability 0.52). MolNFT v1 #128716 on GenesisL1: 3D structure…

PDB: 5NZ3
Type: RNA
Length: 82 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (41-mer)
Ligands: MGX, MG, NA
Pockets: 5 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (41-mer)	rna	41	—	—

Ligands and binding sites

MGX · 1-methylguanidine · ligand · chains A
MG · Magnesium ion · metal · 5 copies · chains A, B
NA · Sodium ion · metal · 4 copies · chains A, B

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

Pockets

5 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	135	0.52	0.81	13	empty
2	138	0.51	0.81	15	MGX, MG
3	61	0.27	0.74	11	MG
4	69	0.26	0.72	10	MG
5	52	0.24	0.74	11	MG

Modifications

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

Compared structures

5NZ3 · The structure of the thermobifida fusca guanidine III riboswitch with methylguanidine · 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 5NZ3 · PDBe 5NZ3

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