Research workbench
The Complex of a novel antibiotic with the Aminoacyl Site of the Bacterial Ribosome Revealed by X-Ray Crystallography.
Analyse The Complex of a novel antibiotic with the Aminoacyl Site of the Bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O9M
- Type
- RNA
- Length
- 42 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Molecule
- Eubacterial a-site
- Ligands
- PA2, P24, 42B, BDG
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eubacterial a-site | rna | 21 | — | — |
Ligands and binding sites
- 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
- BDG · 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose · sugar · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.55 | 0.73 | 33 | P24 |
Interfaces
1 interface between chains.
- A–B · 978 Ų 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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