Research workbench
Complex between kanamycin a and the 16S-rRNA a site.
Analyse Complex between kanamycin a 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
- 2ESI
- Type
- RNA
- Length
- 44 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP *UP*CP*GP*C)-3'
- Ligands
- KAN
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'- R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP *UP*CP*GP*C)-3' | rna | 23 | — | — |
| B | 5'- R(*UP*UP*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
- KAN · Kanamycin A · ligand · 3 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 | 475 | 0.55 | 0.73 | 35 | KAN |
Interfaces
1 interface between chains.
- A–B · 1121 Ų buried · 132 hydrogen bonds · nucleic-nucleic
Compared structures
- 2ESI · Complex between Kanamycin A 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 2ESI · PDBe 2ESI
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