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Crystal structure of a class I PREQ1 riboswitch aptamer (wild-type) complexed with a cognate ligand-derived photoaffinity probe

Analyse Crystal structure of a class I PREQ1 riboswitch aptamer (wild-type) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E9I
Type: RNA
Length: 32 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 33-mer RNA
Ligands: J0C, SO4
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	33-mer RNA	rna	32	—	—

Ligands and binding sites

J0C · 2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl) ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one · ligand · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.31	0.78	13	J0C

Compared structures

7E9I · Crystal structure of a class I PreQ1 riboswitch aptamer (wild-type) complexed with a… · 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 7E9I · PDBe 7E9I

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