MolNFT v1 · #63215 · RNA

Crystal structure of the FMN riboswitch bound to FMN, MN2+ soak.

3F2Y: “Crystal structure of the FMN riboswitch bound to FMN, MN2+ soak.”. X-ray diffraction, 4 ligands (FMN, MG, MN), 5 pockets (best druggability 0.74). MolNFT v1 #63215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F2Y
Type: RNA
Length: 109 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FMN riboswitch
Ligands: FMN, MG, MN, K
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	FMN riboswitch	rna	109	—	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · chains X
MG · Magnesium ion · metal · 11 copies · chains X
MN · Manganese (II) ion · metal · 4 copies · chains X
K · Potassium ion · metal · 2 copies · chains X

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

Pockets

5 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	819	0.74	0.80	44	FMN, K, MG, MN
2	129	0.43	0.77	16	empty
3	120	0.34	0.73	15	MG, MN
4	56	0.29	0.76	7	K
5	50	0.24	0.74	11	MG

Modifications

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

Compared structures

3F2Y · Crystal structure of the FMN riboswitch bound to FMN, Mn2+ soak. · 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 3F2Y · PDBe 3F2Y

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