Research workbench
Crystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-haba group
Analyse Crystal structure of the bacterial ribosomal decoding site in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WRU
- Type
- RNA
- Length
- 42 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP* C)-3')
- Ligands
- SJP, K
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'- R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP* C)-3') | rna | 21 | — | — |
Ligands and binding sites
- SJP · (2R,3R)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-{[3-O-(2,6-diamino-2,3,4,6-tetradeoxy-beta-L-threo-hexopyranosyl)-beta-D-ribofuranosyl]oxy}-2-hydroxycyclohexyl]-3-fluoro-2-hydroxybutanamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains 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 | 395 | 0.52 | 0.73 | 24 | K |
Interfaces
1 interface between chains.
- A–B · 1004 Ų buried · 118 hydrogen bonds · nucleic-nucleic
Compared structures
- 3WRU · Crystal structure of the bacterial ribosomal decoding site in complex with synthetic… · 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 3WRU · PDBe 3WRU
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