Research workbench
Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 ångströms resolution
Analyse Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1POV
- Type
- protein
- Length
- 773 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poliovirus native empty capsid (type 1)
- UniProt
- P03300
- Ligands
- MYR, SPH
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Poliovirus native empty capsid (type 1) | protein | 300 | 14% helix, 35% strand | P03300 |
| 1 | Poliovirus native empty capsid (type 1) | protein | 235 | 8% helix, 35% strand | P03300 |
| 3 | Poliovirus native empty capsid (type 1) | protein | 238 | 9% helix, 30% strand | P03300 |
Ligands and binding sites
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 | 679 | 0.80 | 0.84 | 88 | SPH |
| 2 | 372 | 0.60 | 0.77 | 30 | empty |
| 3 | 57 | 0.50 | 0.86 | 18 | empty |
| 4 | 98 | 0.44 | 0.79 | 20 | empty |
| 5 | 83 | 0.41 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- 1–3 · 3249 Ų buried · 63 hydrogen bonds · protein-protein
- 0–1 · 2614 Ų buried · 44 hydrogen bonds · protein-protein
- 0–3 · 2441 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 lipid (disulfide, myristoylation).
Compared structures
- 1POV · Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of… · the same entry in another collection · chain 0 against 0, 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 P03300
- Elsewhere: RCSB PDB 1POV · PDBe 1POV · UniProt P03300
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