MolNFT v1 · #55371 · RNA

Crystal structure of a F. nucleatum FMN riboswitch - free state

2YIF: “Crystal structure of a F. nucleatum FMN riboswitch - free state”. X-ray diffraction, 2 ligands (MG, K), 6 pockets (best druggability 0.75). MolNFT v1 #55371 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YIF
Type: RNA
Length: 110 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FMN riboswitch
Ligands: MG, K
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	FMN riboswitch	rna	53	—	—
Z	FMN riboswitch	rna	57	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 12 copies · chains X, Z
K · Potassium ion · metal · 2 copies · chains X, Z

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

Pockets

6 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	824	0.75	0.80	42	K, MG
2	156	0.46	0.77	15	empty
3	96	0.33	0.75	12	empty
4	76	0.32	0.76	14	MG
5	95	0.32	0.73	15	MG

Interfaces

1 interface between chains.

X–Z · 2588 Å² buried · 149 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2YIF · Crystal structure of a F. nucleatum FMN riboswitch - Free state · the same entry in another collection · chain X against X, 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 2YIF · PDBe 2YIF

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