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Crystal structure of apramycin bound to a ribosomal RNA a site oligonucleotide

Analyse Crystal structure of apramycin bound to a ribosomal RNA a site oligonucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YRJ
Type: RNA
Length: 45 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacterial 16 S ribosomal RNA a site oligonucleotide
Ligands: AM2, MG, K
Pockets: 1 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacterial 16 S ribosomal RNA a site oligonucleotide	rna	23	—	—
B	Bacterial 16 S ribosomal RNA a site oligonucleotide	rna	22	—	—

Ligands and binding sites

AM2 · Apramycin · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · chains A, B
K · Potassium ion · metal · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	699	0.62	0.73	34	AM2, MG

Interfaces

1 interface between chains.

A–B · 1074 Å² buried · 112 hydrogen bonds · nucleic-nucleic

Compared structures

1YRJ · Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide · 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 1YRJ · PDBe 1YRJ

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