Research workbench
Poliovirus type 3 (strain saukett) stabilized virus-like particle
Analyse Poliovirus type 3 (strain saukett) stabilized virus-like particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O5B
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid proteins; VP4
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q84895, P03302
- Pockets
- 12 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 6% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid proteins | protein | 235 | 6% helix, 30% strand | Q84895 |
| 2 | Capsid proteins | protein | 260 | 7% helix, 34% strand | Q84895 |
| 3 | Capsid proteins | protein | 235 | 7% helix, 26% strand | Q84895 |
| 4 | VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 17 | 0% helix, 0% strand | P03302 |
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.79 | 0.86 | 60 | empty |
| 2 | 107 | 0.55 | 0.84 | 19 | empty |
| 3 | 185 | 0.49 | 0.76 | 38 | empty |
| 4 | 67 | 0.46 | 0.83 | 14 | empty |
| 5 | 95 | 0.44 | 0.79 | 21 | empty |
Interfaces
5 interfaces between chains.
- 1–3 · 3161 Ų buried · 37 hydrogen bonds · protein-protein
- 1–2 · 2042 Ų buried · 17 hydrogen bonds · protein-protein
- 2–3 · 1578 Ų buried · 16 hydrogen bonds · protein-protein
- 3–4 · 377 Ų buried · 3 hydrogen bonds · protein-protein
- 1–4 · 200 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5O5B · Poliovirus type 3 (strain Saukett) stabilized virus-like particle · the same entry in another collection · chain 1 against 1, 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 Q84895
- Every structure of UniProt P03302
- Elsewhere: RCSB PDB 5O5B · PDBe 5O5B · UniProt Q84895 · UniProt P03302
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