Research workbench
The structure of icam-5 triggered enterovirus D68 virus a-particle
Analyse The structure of icam-5 triggered enterovirus D68 virus a-particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AJ2
- Type
- protein
- Length
- 682 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- A0A097F8Q2, A0A0A7X639
- Pockets
- 9 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 7% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 204 | 6% helix, 30% strand | A0A097F8Q2 |
| B | Capsid protein VP2 | protein | 231 | 7% helix, 27% strand | A0A0A7X639 |
| C | Capsid protein VP3 | protein | 247 | 6% helix, 27% strand | — |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.77 | 0.87 | 50 | empty |
| 2 | 164 | 0.62 | 0.84 | 29 | empty |
| 3 | 253 | 0.53 | 0.76 | 39 | empty |
| 4 | 144 | 0.53 | 0.80 | 28 | empty |
| 5 | 82 | 0.42 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3125 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1736 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1688 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6AJ2 · The structure of ICAM-5 triggered Enterovirus D68 virus A-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 A0A097F8Q2
- Every structure of UniProt A0A0A7X639
- Elsewhere: RCSB PDB 6AJ2 · PDBe 6AJ2 · UniProt A0A097F8Q2 · UniProt A0A0A7X639
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