Research workbench
Coxsackievirus B3 full particle at PH7.4 (VP3-234Q)
Analyse Coxsackievirus B3 full particle at PH7.4 (VP3-234Q) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VXH
- Type
- protein
- Length
- 819 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- UniProt
- P03313
- Ligands
- PLM
- Pockets
- 10 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 11% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 268 | 10% helix, 29% strand | P03313 |
| B | Capsid protein VP2 | protein | 256 | 11% helix, 34% strand | P03313 |
| C | Capsid protein VP3 | protein | 238 | 11% helix, 31% strand | P03313 |
| D | Capsid protein VP4 | protein | 57 | 11% helix, 16% strand | P03313 |
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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.79 | 0.85 | 74 | PLM |
| 2 | 87 | 0.52 | 0.84 | 27 | empty |
| 3 | 149 | 0.47 | 0.77 | 29 | empty |
| 4 | 135 | 0.47 | 0.78 | 21 | empty |
| 5 | 86 | 0.46 | 0.81 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4326 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 2151 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1656 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1165 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 889 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7VXH · Coxsackievirus B3 full particle at pH7.4 (VP3-234Q) · 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 P03313
- Elsewhere: RCSB PDB 7VXH · PDBe 7VXH · UniProt P03313
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