MolNFT v1 · #74467 · RNA

Crystal structure of glycine riboswitch, tl-acetate soaked

3OXM · Domain II of glycine riboswitch: “Crystal structure of glycine riboswitch, tl-acetate soaked”. X-ray diffraction, 3 ligands (GLY, MG, TL), 11 pockets (best druggability 0.64). MolNFT v1 #74467 on GenesisL1: 3D structure, binding…

PDB: 3OXM
Type: RNA
Length: 176 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Domain II of glycine riboswitch
Ligands: GLY, MG, TL
Pockets: 11 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Domain II of glycine riboswitch	rna	88	—	—
B	Domain II of glycine riboswitch	rna	88	—	—

Ligands and binding sites

GLY · Glycine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 27 copies · chains A, B
TL · Thallium (I) ion · metal · 10 copies · chains B, A

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

Pockets

11 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	290	0.64	0.82	24	MG
2	445	0.64	0.78	28	TL, MG
3	409	0.61	0.78	23	MG
4	304	0.49	0.73	22	MG
5	192	0.48	0.77	25	GLY, MG

Interfaces

1 interface between chains.

A–B · 1234 Å² buried · 40 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 3 modified (nucleotide modification).

Compared structures

3OXM · crystal structure of glycine riboswitch, Tl-Acetate soaked · 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 3OXM · PDBe 3OXM

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