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Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch

Analyse Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D2G
Type: RNA
Length: 154 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tpp-specific riboswitch
Ligands: TPP, MG
Pockets: 6 · best druggability 0.78

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

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 10 copies · chains B, A

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

Pockets

6 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	1171	0.78	0.81	62	MG, TPP
2	317	0.52	0.74	19	empty
3	276	0.45	0.73	22	empty
4	259	0.45	0.73	22	empty
5	229	0.43	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 330 Å² buried · 9 hydrogen bonds · nucleic-nucleic

Compared structures

3D2G · Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch · 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 3D2G · PDBe 3D2G

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