Research workbench
HIV-1 dis RNA subtype F- mn soaked
Analyse HIV-1 dis RNA subtype F- mn soaked in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y3O
- Type
- RNA
- Length
- 46 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*UP*(5BU) P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP* G)-3'
- Ligands
- MN, NA
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-R(*CP*UP*(5BU) P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP* G)-3' | rna | 23 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains B, A
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 | 670 | 0.61 | 0.73 | 39 | MN, NA |
Interfaces
1 interface between chains.
- A–B · 361 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1Y3O · HIV-1 DIS RNA subtype F- Mn soaked · 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 1Y3O · PDBe 1Y3O
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.