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Multiple capsid-stabilizing protein-RNA and protein-protein interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis
Analyse Multiple capsid-stabilizing protein-RNA and protein-protein interactions… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5APM
- Type
- protein
- Length
- 698 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP3; VP0
- UniProt
- D2IE17
- Pockets
- 13 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 7% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 198 | 4% helix, 15% strand | D2IE17 |
| B | VP3 | protein | 237 | 4% helix, 19% strand | D2IE17 |
| C | VP0 | protein | 263 | 12% helix, 21% strand | D2IE17 |
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.76 | 0.97 | 27 | empty |
| 2 | 591 | 0.72 | 0.80 | 58 | empty |
| 3 | 120 | 0.72 | 0.92 | 32 | empty |
| 4 | 84 | 0.64 | 0.90 | 23 | empty |
| 5 | 220 | 0.63 | 0.82 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3067 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1139 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 747 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5APM · Multiple capsid-stabilizing protein-RNA and protein-protein interactions revealed in a… · 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
- Every structure of UniProt D2IE17
- Elsewhere: RCSB PDB 5APM · PDBe 5APM · UniProt D2IE17
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