MolNFT v1 · #63262 · RNA

Crystal structure of the FMN riboswitch bound to FMN, split RNA.

3F4E: “Crystal structure of the FMN riboswitch bound to FMN, split RNA.”. X-ray diffraction, 3 ligands (FMN, MG, K), 4 pockets (best druggability 0.74). MolNFT v1 #63262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F4E
Type: RNA
Length: 109 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 0.74

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	FMN riboswitch	rna	53	—	—
Y	FMN riboswitch	rna	56	—	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · chains X, Y
MG · Magnesium ion · metal · 13 copies · chains X, Y
K · Potassium ion · metal · chains X

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	841	0.74	0.79	43	MG, FMN
2	129	0.44	0.77	16	empty
3	113	0.35	0.74	14	MG
4	57	0.31	0.77	9	K

Interfaces

1 interface between chains.

X–Y · 2549 Å² buried · 151 hydrogen bonds · nucleic-nucleic

Compared structures

3F4E · Crystal structure of the FMN riboswitch bound to FMN, split RNA. · 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 3F4E · PDBe 3F4E

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