MolNFT v1 · #146623 · RNA

Crystal structure of the FMN riboswitch bound to BRX1354 split RNA

6DN2 · RNA riboswitch: “Crystal structure of the FMN riboswitch bound to BRX1354 split RNA”. X-ray diffraction, 3 ligands (GZG, MG, K), 6 pockets (best druggability 0.71). MolNFT v1 #146623 on GenesisL1: 3D structure, binding sites and…

PDB: 6DN2
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: GZG, MG, K
Pockets: 6 · best druggability 0.71

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

GZG · 4-{benzyl[2-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)ethyl]amino}butanoic acid · ligand · chains X, Y
MG · Magnesium ion · metal · 6 copies · chains X, Y
K · Potassium ion · metal · chains Y

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	502	0.71	0.82	26	GZG, K
2	196	0.50	0.78	18	MG
3	120	0.42	0.77	14	empty
4	122	0.34	0.73	14	MG
5	50	0.30	0.77	9	MG

Interfaces

1 interface between chains.

X–Y · 2601 Å² buried · 151 hydrogen bonds · nucleic-nucleic

Compared structures

6DN2 · Crystal structure of the FMN riboswitch bound to BRX1354 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 6DN2 · PDBe 6DN2

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