MolNFT v1 · #31864 · RNA
Structure of HIV-1(MAL) genomic RNA dis
2B8S · 5'- R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP…: “Structure of HIV-1(MAL) genomic RNA dis”. X-ray diffraction, 3 ligands (MG, NA, SO4), 1 pocket (best druggability 0.63). MolNFT v1 #31864 on GenesisL1: 3D structure…
- PDB
- 2B8S
- Type
- RNA
- Length
- 46 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP *CP*AP*AP*G)-3'
- Ligands
- MG, NA, SO4
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'- R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP *CP*AP*AP*G)-3' | rna | 23 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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 | 766 | 0.63 | 0.74 | 40 | MG, NA, SO4 |
Interfaces
1 interface between chains.
- A–B · 364 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Compared structures
- 2B8S · Structure of HIV-1(MAL) genomic RNA DIS · 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 2B8S · PDBe 2B8S
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