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Structure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine pyrophosphate

Analyse Structure of the thiamine pyrophosphate-specific riboswitch bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D2X
Type: RNA
Length: 154 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tpp-specific riboswitch
Ligands: D2X, MG
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tpp-specific riboswitch	rna	77	—	—

Ligands and binding sites

D2X · 3-[(4-hydroxy-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 13 copies · chains A, B

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

Pockets

8 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	673	0.73	0.81	42	D2X, MG
2	508	0.69	0.80	27	D2X, MG
3	349	0.53	0.74	19	empty
4	216	0.42	0.73	15	empty
5	148	0.42	0.76	21	empty

Interfaces

1 interface between chains.

A–B · 343 Å² buried · 11 hydrogen bonds · nucleic-nucleic

Compared structures

3D2X · Structure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3D2X · PDBe 3D2X

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