Research workbench
Cryo-EM structure of coxsackievirus B1 empty particle
Analyse Cryo-EM structure of coxsackievirus B1 empty particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DPG
- Type
- protein
- Length
- 682 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion protein 1; VP2; VP3
- UniProt
- W8GTF7, A0A2S0RQC2, L7UV52
- Pockets
- 10 · best druggability 0.61
Structure
electron microscopy · 3 distinct chains · 6% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Virion protein 1 | protein | 217 | 7% helix, 29% strand | W8GTF7 |
| 2 | VP2 | protein | 233 | 10% helix, 29% strand | A0A2S0RQC2 |
| 3 | VP3 | protein | 232 | 2% helix, 24% strand | L7UV52 |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.61 | 0.82 | 25 | empty |
| 2 | 91 | 0.43 | 0.79 | 19 | empty |
| 3 | 80 | 0.39 | 0.78 | 17 | empty |
| 4 | 114 | 0.39 | 0.75 | 17 | empty |
| 5 | 57 | 0.36 | 0.78 | 13 | empty |
Interfaces
3 interfaces between chains.
- 1–3 · 2732 Ų buried · 30 hydrogen bonds · protein-protein
- 1–2 · 1786 Ų buried · 24 hydrogen bonds · protein-protein
- 2–3 · 1513 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7DPG · Cryo-EM structure of Coxsackievirus B1 empty particle · the same entry in another collection · chain 1 against 1, 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 W8GTF7
- Every structure of UniProt A0A2S0RQC2
- Every structure of UniProt L7UV52
- Elsewhere: RCSB PDB 7DPG · PDBe 7DPG · UniProt W8GTF7 · UniProt A0A2S0RQC2 · UniProt L7UV52
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