Research workbench
The structure of HRV14 when complexed with pleconaril
Analyse The structure of HRV14 when complexed with pleconaril in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NA1
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein VP1; Coat protein VP2; Coat protein VP3; Coat protein VP4
- UniProt
- P03303
- Ligands
- W11
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coat protein VP1 | protein | 273 | 11% helix, 33% strand | P03303 |
| B | Coat protein VP2 | protein | 255 | 15% helix, 37% strand | P03303 |
| C | Coat protein VP3 | protein | 236 | 10% helix, 31% strand | P03303 |
| D | Coat protein VP4 | protein | 40 | 18% helix, 3% strand | P03303 |
Ligands and binding sites
- W11 · 3-{3,5-dimethyl-4-[3-(3-methyl-isoxazol-5-yl)-propoxy]-phenyl}-5-trifluoromethyl-[1,2,4]oxadiazole · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.79 | 0.91 | 41 | W11 |
| 2 | 212 | 0.51 | 0.76 | 36 | empty |
| 3 | 132 | 0.46 | 0.78 | 24 | empty |
| 4 | 133 | 0.44 | 0.76 | 29 | empty |
| 5 | 110 | 0.38 | 0.74 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4118 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 2124 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1717 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 957 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 909 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1NA1 · The structure of HRV14 when complexed with Pleconaril · 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 P03303
- Elsewhere: RCSB PDB 1NA1 · PDBe 1NA1 · UniProt P03303
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