MolNFT v1 · #146622 · RNA

Crystal structure of the FMN riboswitch bound to BRX1151 split RNA

6DN1 · RNA riboswitch: “Crystal structure of the FMN riboswitch bound to BRX1151 split RNA”. X-ray diffraction, 3 ligands (GZ7, MG, K), 6 pockets (best druggability 0.74). MolNFT v1 #146622 on GenesisL1: 3D structure, binding sites and…

PDB: 6DN1
Type: RNA
Length: 111 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA riboswitch; RNA (57-mer)
Ligands: GZ7, MG, K
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	RNA riboswitch	rna	54	—	—
Z	RNA (57-mer)	rna	57	—	—

Ligands and binding sites

GZ7 · 10-(6-carboxyhexyl)-8-(cyclopentylamino)-2,4-dihydroxy-7-methylbenzo[g]pteridin-10-ium · ligand · chains X, Z
MG · Magnesium ion · metal · 6 copies · chains X, Z
K · Potassium ion · metal · chains Z

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

Pockets

6 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	837	0.74	0.80	42	MG, GZ7, K
2	132	0.41	0.76	14	empty
3	58	0.32	0.78	11	MG
4	78	0.29	0.73	10	MG
5	54	0.27	0.75	14	empty

Interfaces

1 interface between chains.

X–Z · 2632 Å² buried · 156 hydrogen bonds · nucleic-nucleic

Compared structures

6DN1 · Crystal structure of the FMN riboswitch bound to BRX1151 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 6DN1 · PDBe 6DN1

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