MolNFT v1 · #16798 · RNA

The complex of a novel antibiotic with the aminoacyl site of the bacterial ribosome revealed by X-ray crystallography.

1O9M · Eubacterial a-site: “The complex of a novel antibiotic with the aminoacyl site of the bacterial ribosome revealed by X-ray…”. X-ray diffraction, 4 ligands (BDG, PA2, P24), 1 pocket (best druggability 0.55). MolNFT v1 #16798 on…

PDB: 1O9M
Type: RNA
Length: 42 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eubacterial a-site
Ligands: BDG, PA2, P24, 42B
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Eubacterial a-site	rna	21	—	—

Ligands and binding sites

BDG · 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose · ligand · chains A, B
PA2 · Paromomycin (ring 2) · ligand · chains A, B
P24 · 1-(aminoethyl)amino-4-aminobutane · ligand · chains A, B
42B · 4-amino-2-hydroxybutanoic acid · ligand · 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	482	0.55	0.73	33	P24

Interfaces

1 interface between chains.

A–B · 978 Å² buried · 106 hydrogen bonds · nucleic-nucleic

Compared structures

1O9M · The Complex of a novel antibiotic with the Aminoacyl Site of the Bacterial Ribosome… · 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 1O9M · PDBe 1O9M

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