Research workbench
Cryoem structure of human enterovirus D68 emptied particle (after incubation with low molecular weight heparin)
Analyse Cryoem structure of human enterovirus D68 emptied particle (after incubation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CV4
- Type
- protein
- Length
- 659 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
- 7 · best druggability 0.69
Structure
electron microscopy · 3 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Viral protein 1 | protein | 225 | 8% helix, 40% strand | A0A0X7Z9B1 |
| B | Viral protein 3 | protein | 234 | 9% helix, 32% strand | E9RIT6 |
| C | Viral protein 2 | protein | 200 | 14% helix, 38% strand | A0A097ZN88 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.69 | 0.85 | 27 | empty |
| 2 | 96 | 0.40 | 0.77 | 18 | empty |
| 3 | 73 | 0.37 | 0.77 | 18 | empty |
| 4 | 88 | 0.37 | 0.76 | 16 | empty |
| 5 | 103 | 0.37 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3394 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 1867 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1753 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6CV4 · CryoEM structure of human enterovirus D68 emptied particle (after incubation with low… · 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 6CV4 · PDBe 6CV4 · UniProt A0A0X7Z9B1 · UniProt E9RIT6 · UniProt A0A097ZN88
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