MolNFT v1 · #146643 · RNA

Prpp riboswitch bound to prpp, ligand-free structure

6DNR: “Prpp riboswitch bound to prpp, ligand-free structure”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.69). MolNFT v1 #146643 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DNR
Type: RNA
Length: 107 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prpp riboswitch
Ligands: MG
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prpp riboswitch	rna	107	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A

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

Pockets

4 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	932	0.69	0.75	50	MG
2	522	0.65	0.78	37	MG
3	98	0.37	0.76	14	empty
4	53	0.34	0.79	9	empty

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

6DNR · PRPP Riboswitch bound to PRPP, ligand-free structure · the same entry in another collection · chain A against A, 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 6DNR · PDBe 6DNR

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.