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Saccharide-RNA recognition in the neomycin B / RNA aptamer complex

Analyse Saccharide-RNA recognition in the neomycin B / RNA aptamer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NEM
Type: RNA
Length: 23 nucleotides
Chains: 1
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP *AP*GP*UP*CP*C)-3'
Ligands: BDR, IDG, BDG, NEB
Pockets: 1 · best druggability 0.49

Structure

solution nmr · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-R(GPGPAPCPUPGPGPGPCPGPAPGPAPAPGPUPUPUP APGPUPCP*C)-3'	rna	23	—	—

Ligands and binding sites

BDR · beta-D-ribofuranose · ligand · chains A
IDG · 2,6-diamino-2,6-dideoxy-beta-L-idopyranose · ligand · chains A
BDG · 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose · ligand · chains A
NEB · 2-deoxy-D-streptamine · ligand · 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	196	0.49	0.77	15	BDR, BDG, NEB

Compared structures

1NEM · Saccharide-RNA recognition in the neomycin B / RNA aptamer complex · 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 1NEM · PDBe 1NEM

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