Research workbench
Structure of HRV2 capsid complexed with antiviral compound BTA798
Analyse Structure of HRV2 capsid complexed with antiviral compound BTA798 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VDD
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein VP1; Protein VP2; Protein VP3; Protein VP4
- UniProt
- P04936
- Ligands
- BT8
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein VP1 | protein | 280 | 9% helix, 31% strand | P04936 |
| B | Protein VP2 | protein | 251 | 14% helix, 38% strand | P04936 |
| C | Protein VP3 | protein | 237 | 9% helix, 32% strand | P04936 |
| D | Protein VP4 | protein | 36 | 8% helix, 3% strand | P04936 |
Ligands and binding sites
- BT8 · 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.82 | 0.93 | 38 | BT8 |
| 2 | 292 | 0.56 | 0.77 | 30 | empty |
| 3 | 272 | 0.52 | 0.75 | 42 | empty |
| 4 | 139 | 0.52 | 0.80 | 35 | empty |
| 5 | 131 | 0.51 | 0.80 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4228 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 2131 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1680 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 915 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 724 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3VDD · Structure of HRV2 capsid complexed with antiviral compound BTA798 · 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 P04936
- Elsewhere: RCSB PDB 3VDD · PDBe 3VDD · UniProt P04936
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.