Research workbench
Cryoem structure of human enterovirus D68 full particle (after incubation with low molecular weight heparin)
Analyse Cryoem structure of human enterovirus D68 full particle (after incubation with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CV5
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viral protein 1; Viral protein 3; Viral protein 2; Viral protein 4
- UniProt
- A0A0X7Z9B1, E9RIT6, A0A097ZN88, A0A0P0DH17
- Pockets
- 12 · best druggability 0.67
Structure
electron microscopy · 4 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Viral protein 1 | protein | 290 | 8% helix, 32% strand | A0A0X7Z9B1 |
| B | Viral protein 3 | protein | 247 | 7% helix, 30% strand | E9RIT6 |
| C | Viral protein 2 | protein | 237 | 13% helix, 37% strand | A0A097ZN88 |
| D | Viral protein 4 | protein | 30 | 23% helix, 10% strand | A0A0P0DH17 |
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 | 208 | 0.67 | 0.85 | 34 | empty |
| 2 | 222 | 0.52 | 0.76 | 34 | empty |
| 3 | 158 | 0.50 | 0.78 | 27 | empty |
| 4 | 131 | 0.47 | 0.78 | 25 | empty |
| 5 | 151 | 0.46 | 0.77 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4807 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 2114 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1840 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 932 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 833 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6CV5 · CryoEM structure of human enterovirus D68 full 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
- Every structure of UniProt A0A0P0DH17
- Elsewhere: RCSB PDB 6CV5 · PDBe 6CV5 · UniProt A0A0X7Z9B1 · UniProt E9RIT6 · UniProt A0A097ZN88 · UniProt A0A0P0DH17
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