MolNFT v1 · #12208 · RNA
HIV-1(MAL) RNA dimerization initiation site
1K9W · HIV-1 DIS(MAL)UU RNA: “HIV-1(MAL) RNA dimerization initiation site”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.67). MolNFT v1 #12208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K9W
- Type
- RNA
- Length
- 92 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 DIS(MAL)UU RNA
- Ligands
- MG
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HIV-1 DIS(MAL)UU RNA | rna | 23 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.67 | 0.74 | 40 | empty |
| 2 | 907 | 0.66 | 0.74 | 38 | empty |
| 3 | 160 | 0.38 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 385 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- A–B · 365 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 349 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 1K9W · HIV-1(MAL) RNA Dimerization Initiation Site · 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 1K9W · PDBe 1K9W
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.