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Crystal structure of the FMN riboswitch bound to BRX1555 split RNA

Analyse Crystal structure of the FMN riboswitch bound to BRX1555 split RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DN3
Type: RNA
Length: 109 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA riboswitch; RNA (56-mer)
Ligands: GZ4, MG, K, CL
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains.

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

Ligands and binding sites

GZ4 · 7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium · ligand · chains X, Y
MG · Magnesium ion · metal · 7 copies · chains X, Y
K · Potassium ion · metal · chains Y
CL · Chloride ion · ion · chains X, Y

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	687	0.73	0.80	42	CL, MG, GZ4, K
2	123	0.44	0.78	14	empty
3	117	0.35	0.73	11	MG
4	73	0.32	0.76	14	empty

Interfaces

1 interface between chains.

X–Y · 2616 Å² buried · 162 hydrogen bonds · nucleic-nucleic

Compared structures

6DN3 · Crystal structure of the FMN riboswitch bound to BRX1555 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 6DN3 · PDBe 6DN3

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