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Crystal structure of a F. nucleatum FMN riboswitch bound to wg-3

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

PDB: 6BFB
Type: RNA
Length: 109 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (54-mer); RNA (56-mer)
Ligands: DKM, MG
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	RNA (54-mer)	rna	53	—	—
Y	RNA (56-mer)	rna	56	—	—

Ligands and binding sites

DKM · 5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic acid · ligand · chains X, Y
MG · Magnesium 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	793	0.74	0.80	40	DKM, MG
2	123	0.43	0.78	13	empty
3	112	0.35	0.74	15	empty
4	61	0.32	0.77	10	empty

Interfaces

1 interface between chains.

X–Y · 2644 Å² buried · 166 hydrogen bonds · nucleic-nucleic

Compared structures

6BFB · Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3 · 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 6BFB · PDBe 6BFB

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