MolNFT v1 · #36673 · RNA
HIV-1 dis kissing-loop in complex with neomycin
2FCY · HIV-1 dis RNA: “HIV-1 dis kissing-loop in complex with neomycin”. X-ray diffraction, 4 ligands (NMY, K, CL), 1 pocket (best druggability 0.63). MolNFT v1 #36673 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2FCY
- Type
- RNA
- Length
- 46 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 dis RNA
- Ligands
- NMY, K, CL, SO4
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 dis RNA | rna | 23 | — | — |
Ligands and binding sites
- NMY · Neomycin · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · chains B
- SO4 · Sulfate ion · ion · 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 | 816 | 0.63 | 0.73 | 40 | K, NMY |
Interfaces
1 interface between chains.
- A–B · 369 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2FCY · HIV-1 DIS kissing-loop in complex with Neomycin · 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 2FCY · PDBe 2FCY
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