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Crystal structure of a F. nucleatum FMN riboswitch bound to FMN

Analyse Crystal structure of a F. nucleatum FMN riboswitch bound to FMN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YIE
Type: RNA
Length: 111 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FMN riboswitch
Ligands: FMN, MG, K
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	FMN riboswitch	rna	54	—	—
Z	FMN riboswitch	rna	57	—	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · chains X, Z
MG · Magnesium ion · metal · 14 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

4 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	863	0.75	0.80	46	MG, K, FMN
2	104	0.42	0.78	16	empty
3	99	0.31	0.73	14	MG
4	53	0.27	0.75	14	MG

Interfaces

1 interface between chains.

X–Z · 2649 Å² buried · 153 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2YIE · Crystal structure of a F. nucleatum FMN riboswitch bound to FMN · the same entry in another collection · chain Z against Z, 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 2YIE · PDBe 2YIE

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