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Crystal structure of glycine riboswitch with single mutation

Analyse Crystal structure of glycine riboswitch with single mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OXB
Type: RNA
Length: 175 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Domain II of glycine riboswitch
Ligands: MG
Pockets: 10 · best druggability 0.71

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	87	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 28 copies · chains A, B

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

Pockets

10 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	540	0.71	0.81	39	MG
2	471	0.64	0.78	27	MG
3	404	0.61	0.78	23	MG
4	311	0.49	0.73	23	MG
5	156	0.45	0.77	21	MG

Interfaces

1 interface between chains.

A–B · 1229 Å² buried · 42 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3OXB · Crystal structure of glycine riboswitch with single mutation · 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 3OXB · PDBe 3OXB

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