Research workbench
Echovirus 30 F-particle
Analyse Echovirus 30 F-particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C9S
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Echovirus E30
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- Q33C85
- Ligands
- SPH
- Pockets
- 12 · best druggability 0.78
Structure
electron microscopy · resolution 2.9 · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 276 | 10% helix, 31% strand | — |
| B | VP2 | protein | 251 | 9% helix, 38% strand | — |
| C | VP3 | protein | 238 | 7% helix, 32% strand | — |
| D | VP4 | protein | 57 | 11% helix, 16% strand | Q33C85 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.78 | 0.84 | 74 | SPH |
| 2 | 122 | 0.51 | 0.81 | 38 | empty |
| 3 | 130 | 0.47 | 0.78 | 22 | empty |
| 4 | 130 | 0.47 | 0.78 | 27 | empty |
| 5 | 82 | 0.41 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4296 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 2105 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1667 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1249 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 930 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7C9S · Echovirus 30 F-particle · 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 Q33C85
- Elsewhere: RCSB PDB 7C9S · PDBe 7C9S · UniProt Q33C85
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