MolNFT v1 · #146579 · RNA

Prpp riboswitch bound to prpp, iridium-hexamine soaked structure

6DLR: “Prpp riboswitch bound to prpp, iridium-hexamine soaked structure”. X-ray diffraction, 4 ligands (IRI, PRP, MG), 3 pockets (best druggability 0.71). MolNFT v1 #146579 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DLR
Type: RNA
Length: 107 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prpp riboswitch
Ligands: IRI, PRP, MG, K
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 18 copies · chains A
PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · chains A
MG · Magnesium ion · metal · 3 copies · chains A
K · Potassium ion · metal · 3 copies · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

3 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	631	0.71	0.80	36	PRP, IRI, MG
2	913	0.70	0.76	49	IRI
3	174	0.47	0.77	16	IRI

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

6DLR · PRPP Riboswitch bound to PRPP, iridium-hexamine soaked 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 6DLR · PDBe 6DLR

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