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The crystal structure of swine vesicular disease virus
Analyse The crystal structure of swine vesicular disease virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OOP
- Type
- protein
- Length
- 819 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
- P13900
- Ligands
- SPH, MYR
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coat protein VP1 | protein | 271 | 10% helix, 31% strand | P13900 |
| B | Coat protein VP2 | protein | 252 | 10% helix, 38% strand | P13900 |
| C | Coat protein VP3 | protein | 238 | 9% helix, 31% strand | P13900 |
| D | Coat protein VP4 | protein | 58 | 12% helix, 9% strand | P13900 |
Ligands and binding sites
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 | 522 | 0.79 | 0.85 | 63 | SPH |
| 2 | 89 | 0.53 | 0.84 | 23 | empty |
| 3 | 144 | 0.48 | 0.78 | 21 | empty |
| 4 | 106 | 0.43 | 0.78 | 21 | empty |
| 5 | 118 | 0.43 | 0.77 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4329 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 2172 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1592 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1188 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 870 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1OOP · The Crystal Structure of Swine Vesicular Disease Virus · 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 P13900
- Elsewhere: RCSB PDB 1OOP · PDBe 1OOP · UniProt P13900
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