Research workbench
Complex between paromomycin derivative JS5-39 and the 16S-rRNA a-site.
Analyse Complex between paromomycin derivative JS5-39 and the 16S-rRNA a-site. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BE0
- Type
- RNA
- Length
- 42 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP *UP*CP*GP*C)-3'
- Ligands
- JS5
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP *UP*CP*GP*C)-3' | rna | 21 | — | — |
Ligands and binding sites
- JS5 · (2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-((2R,3R,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-diamino-2-((2S,3R,4R,5S,6R)-3-amino-4 ,5-dihydroxy-6-(hydroxymethyl)-tetrahydro-2H-pyran-2-yloxy)-6-hydroxycyclohexyloxy)-2-(hydroxymethyl)-4-(2-((R)-piperidi N-3-ylmethylamino)ethoxy)-tetrahydrofuran-3-yloxy)-tetrahydro-2H-pyran-3,4-diol · ligand · 2 copies · 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 | 533 | 0.56 | 0.73 | 29 | JS5 |
Interfaces
1 interface between chains.
- A–B · 990 Ų buried · 88 hydrogen bonds · nucleic-nucleic
Compared structures
- 2BE0 · Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site. · 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 2BE0 · PDBe 2BE0
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