Research workbench
Cryoem structure of human enterovirus D68 emptied particle
Analyse Cryoem structure of human enterovirus D68 emptied particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CV3
- Type
- protein
- Length
- 672 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viral protein 1; Viral protein 3; Viral protein 2
- UniProt
- A0A0X7Z9B1, E9RIT6, A0A097ZN88
- Pockets
- 9 · best druggability 0.53
Structure
electron microscopy · 3 distinct chains · 7% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Viral protein 1 | protein | 224 | 7% helix, 31% strand | A0A0X7Z9B1 |
| B | Viral protein 3 | protein | 237 | 5% helix, 30% strand | E9RIT6 |
| C | Viral protein 2 | protein | 211 | 10% helix, 32% strand | A0A097ZN88 |
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 | 55 | 0.53 | 0.88 | 16 | empty |
| 2 | 171 | 0.50 | 0.78 | 23 | empty |
| 3 | 128 | 0.48 | 0.79 | 18 | empty |
| 4 | 100 | 0.43 | 0.78 | 16 | empty |
| 5 | 75 | 0.40 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3315 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 1851 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1808 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6CV3 · CryoEM structure of human enterovirus D68 emptied 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 A0A0X7Z9B1
- Every structure of UniProt E9RIT6
- Every structure of UniProt A0A097ZN88
- Elsewhere: RCSB PDB 6CV3 · PDBe 6CV3 · UniProt A0A0X7Z9B1 · UniProt E9RIT6 · UniProt A0A097ZN88
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