Research workbench
Crystal structure of a mosquito-borne flavivirus dumbbell RNA
Analyse Crystal structure of a mosquito-borne flavivirus dumbbell RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KGA
- Type
- RNA
- Length
- 179 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (90-mer)
- Ligands
- IRI
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (90-mer) | rna | 89 | — | — |
| B | RNA (90-mer) | rna | 90 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 44 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.69 | 0.75 | 47 | IRI |
| 2 | 992 | 0.68 | 0.75 | 52 | IRI |
| 3 | 387 | 0.63 | 0.79 | 21 | IRI |
| 4 | 339 | 0.59 | 0.78 | 19 | IRI |
| 5 | 109 | 0.33 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 70 hydrogen bonds · nucleic-nucleic
Compared structures
- 7KGA · Crystal structure of a mosquito-borne flavivirus dumbbell RNA · 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 7KGA · PDBe 7KGA
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