Research workbench
Cryo-EM structure of full echovirus 6 particle at pH 5.5
Analyse Cryo-EM structure of full echovirus 6 particle at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ILN
- Type
- protein
- Length
- 823 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- Ligands
- SPH
- Pockets
- 12 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 275 | 8% helix, 29% strand | — |
| B | Capsid protein VP2 | protein | 252 | 8% helix, 33% strand | — |
| C | Capsid protein VP3 | protein | 238 | 8% helix, 29% strand | — |
| D | Capsid protein VP4 | protein | 58 | 5% helix, 14% strand | — |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.79 | 0.85 | 86 | SPH |
| 2 | 90 | 0.48 | 0.82 | 18 | empty |
| 3 | 233 | 0.46 | 0.73 | 36 | empty |
| 4 | 122 | 0.46 | 0.78 | 20 | empty |
| 5 | 91 | 0.45 | 0.80 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4231 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2136 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1601 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1189 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 947 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6ILN · Cryo-EM structure of full Echovirus 6 particle at PH 5.5 · 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 6ILN · PDBe 6ILN
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