Research workbench
Coxsackievirus B3 full particle at PH7.4 (VP3-234E)
Analyse Coxsackievirus B3 full particle at PH7.4 (VP3-234E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W17
- Type
- protein
- Length
- 819 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- Ligands
- PLM
- Pockets
- 12 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 268 | 9% helix, 30% strand | — |
| B | VP2 | protein | 256 | 8% helix, 38% strand | — |
| C | VP3 | protein | 238 | 13% helix, 32% strand | — |
| D | VP4 | protein | 57 | 0% helix, 16% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.79 | 0.86 | 62 | PLM |
| 2 | 52 | 0.70 | 0.98 | 15 | empty |
| 3 | 156 | 0.53 | 0.80 | 39 | empty |
| 4 | 165 | 0.51 | 0.78 | 22 | empty |
| 5 | 116 | 0.50 | 0.80 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4346 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 2220 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1558 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1178 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 893 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7W17 · Coxsackievirus B3 full particle at pH7.4 (VP3-234E) · 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
- Elsewhere: RCSB PDB 7W17 · PDBe 7W17
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