Research workbench
Asite RNA + designer antibiotic
Analyse Asite RNA + designer antibiotic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F4U
- Type
- RNA
- Length
- 42 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- R(*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP *GP*C)-3'
- Ligands
- AB6
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'- R(*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
- AB6 · (2R)-4-amino-N-((1R,2S,3R,4R,5S)-5-amino-4-[(2-amino-2-deoxy-alpha-D-glucopyranosyl)oxy]-2-{2-[(3-aminopropyl)amino]ethoxy}-3-hydroxycyclohexyl)-2-hydroxybutanamide · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.53 | 0.73 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 976 Ų buried · 110 hydrogen bonds · nucleic-nucleic
Compared structures
- 2F4U · Asite RNA + designer antibiotic · 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 2F4U · PDBe 2F4U
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