Research workbench
Cryoem structure of human enterovirus D68 emptied particle (pH 5.5 and room temperature)
Analyse Cryoem structure of human enterovirus D68 emptied particle (pH 5.5 and room… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CSA
- Type
- protein
- Length
- 642 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
- A0A097BW12, A0A1I9KXX3
- Pockets
- 7 · best druggability 0.67
Structure
electron microscopy · 3 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Viral protein 1 | protein | 199 | 9% helix, 39% strand | A0A097BW12 |
| B | Viral protein 3 | protein | 227 | 7% helix, 27% strand | A0A097BW12 |
| C | Viral protein 2 | protein | 216 | 10% helix, 30% strand | A0A1I9KXX3 |
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 | 182 | 0.67 | 0.86 | 26 | empty |
| 2 | 111 | 0.39 | 0.75 | 21 | empty |
| 3 | 103 | 0.36 | 0.74 | 17 | empty |
| 4 | 76 | 0.36 | 0.76 | 15 | empty |
| 5 | 69 | 0.32 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2280 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1765 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1711 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6CSA · CryoEM structure of human enterovirus D68 emptied particle (pH 5.5 and room temperature) · 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 A0A097BW12
- Every structure of UniProt A0A1I9KXX3
- Elsewhere: RCSB PDB 6CSA · PDBe 6CSA · UniProt A0A097BW12 · UniProt A0A1I9KXX3
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