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The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA
Analyse The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F8V
- Type
- protein + RNA
- Length
- 1,071 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA; Mature capsid protein beta; Mature capsid protein gamma
- UniProt
- Q9J7Z0
- Ligands
- CA, SO4
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA | rna | 25 | — | — |
| A | Mature capsid protein beta | protein | 355 | 11% helix, 38% strand | Q9J7Z0 |
| D | Mature capsid protein gamma | protein | 25 | 48% helix, 0% strand | Q9J7Z0 |
| B | Mature capsid protein beta | protein | 313 | 16% helix, 41% strand | Q9J7Z0 |
| E, F | Mature capsid protein gamma | protein | 21 | 52% helix, 14% strand | Q9J7Z0 |
| C | Mature capsid protein beta | protein | 311 | 15% helix, 41% strand | Q9J7Z0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.87 | 0.90 | 57 | empty |
| 2 | 318 | 0.86 | 0.96 | 43 | SO4 |
| 3 | 879 | 0.78 | 0.81 | 63 | empty |
| 4 | 317 | 0.65 | 0.81 | 48 | empty |
| 5 | 110 | 0.53 | 0.83 | 22 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2788 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2337 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1863 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1004 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 814 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1F8V · The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA · the same entry in another collection · chain R against R, 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
- Every structure of UniProt Q9J7Z0
- Elsewhere: RCSB PDB 1F8V · PDBe 1F8V · UniProt Q9J7Z0
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