MolNFT v1 · #189826 · protein
Coxsackievirus B3 full particle at PH7.4 (VP3-234N)
7VY0 · Capsid protein VP1: “Coxsackievirus B3 full particle at PH7.4 (VP3-234N)”. Electron microscopy, 1 ligand (PLM), 10 pockets (best druggability 0.79). MolNFT v1 #189826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VY0
- Type
- protein
- Length
- 818 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
- Ligands
- PLM
- Pockets
- 10 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 268 | 10% helix, 30% strand | — |
| B | Capsid protein VP2 | protein | 255 | 11% helix, 35% strand | — |
| C | Capsid protein VP3 | protein | 238 | 9% helix, 32% strand | — |
| D | Capsid protein 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
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 | 569 | 0.79 | 0.85 | 66 | PLM |
| 2 | 159 | 0.52 | 0.79 | 22 | empty |
| 3 | 75 | 0.48 | 0.83 | 21 | empty |
| 4 | 68 | 0.47 | 0.83 | 18 | empty |
| 5 | 124 | 0.46 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4344 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2123 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1707 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1133 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 906 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7VY0 · Coxsackievirus B3 full particle at pH7.4 (VP3-234N) · 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 7VY0 · PDBe 7VY0
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