MolNFT v1 · #91914 · RNA

Crystal structure of the cobalamin riboswitch aptamer domain

4FRG: “Crystal structure of the cobalamin riboswitch aptamer domain”. X-ray diffraction, 3 ligands (I2A, IR3, MG), 6 pockets (best druggability 0.70). MolNFT v1 #91914 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FRG
Type: RNA
Length: 168 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cobalamin riboswitch aptamer domain
Ligands: I2A, IR3, MG
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, X	Cobalamin riboswitch aptamer domain	rna	84	—	—

Ligands and binding sites

I2A · Hydroxocobalamin · ligand · 2 copies · chains B, X
IR3 · Iridium (III) ion · metal · 17 copies · chains B, X
MG · Magnesium ion · metal · 16 copies · chains B, X

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.70	0.76	65	IR3, MG
2	489	0.62	0.77	26	IR3, MG
3	475	0.59	0.75	25	IR3, MG
4	175	0.48	0.78	17	MG
5	184	0.48	0.77	18	MG

Interfaces

1 interface between chains.

B–X · 218 Å² buried · 6 hydrogen bonds · nucleic-nucleic

Compared structures

4FRG · Crystal structure of the cobalamin riboswitch aptamer domain · the same entry in another collection · chain B against B, 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 4FRG · PDBe 4FRG

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