Research workbench
Cryoem structure of the full virion of a human rhinovirus C
Analyse Cryoem structure of the full virion of a human rhinovirus C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K0U
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP3; Capsid protein VP2; Capsid protein VP4
- UniProt
- E5D8F2
- Pockets
- 9 · best druggability 0.59
Structure
electron microscopy · 4 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 263 | 10% helix, 28% strand | E5D8F2 |
| B | Capsid protein VP3 | protein | 235 | 9% helix, 32% strand | E5D8F2 |
| C | Capsid protein VP2 | protein | 255 | 12% helix, 36% strand | E5D8F2 |
| D | Capsid protein VP4 | protein | 39 | 8% helix, 3% strand | E5D8F2 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.59 | 0.78 | 51 | empty |
| 2 | 221 | 0.51 | 0.76 | 39 | empty |
| 3 | 106 | 0.45 | 0.79 | 22 | empty |
| 4 | 84 | 0.43 | 0.79 | 21 | empty |
| 5 | 102 | 0.40 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4004 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 2200 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1612 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 708 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 624 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5K0U · CryoEM structure of the full virion of a human rhinovirus C · 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 E5D8F2
- Elsewhere: RCSB PDB 5K0U · PDBe 5K0U · UniProt E5D8F2
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