Research workbench
Poliovirus type 3 (strain saukett) stabilized virus-like particle in complex with the pocket factor compound GPP3
Analyse Poliovirus type 3 (strain saukett) stabilized virus-like particle in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O5P
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid proteins, VP1; Capsid proteins, VP2; Capsid proteins, VP3; Genome polyprotein
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q84895, P03302
- Ligands
- 9LW
- Pockets
- 11 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 6% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid proteins, VP1 | protein | 235 | 7% helix, 29% strand | Q84895 |
| 2 | Capsid proteins, VP2 | protein | 260 | 7% helix, 28% strand | Q84895 |
| 3 | Capsid proteins, VP3 | protein | 235 | 4% helix, 23% strand | Q84895 |
| 4 | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 17 | 0% helix, 0% strand | P03302 |
Ligands and binding sites
- 9LW · 1-[5-[4-(ethoxyiminomethyl)phenoxy]-3-methyl-pentyl]-3-pyridin-4-yl-imidazol-2-one · ligand · chains 1, 3
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 | 499 | 0.80 | 0.87 | 63 | 9LW |
| 2 | 125 | 0.56 | 0.83 | 24 | empty |
| 3 | 64 | 0.43 | 0.82 | 15 | empty |
| 4 | 109 | 0.40 | 0.75 | 17 | empty |
| 5 | 115 | 0.39 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- 1–3 · 3165 Ų buried · 34 hydrogen bonds · protein-protein
- 1–2 · 2066 Ų buried · 21 hydrogen bonds · protein-protein
- 2–3 · 1639 Ų buried · 15 hydrogen bonds · protein-protein
- 3–4 · 340 Ų buried · 2 hydrogen bonds · protein-protein
- 1–4 · 224 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5O5P · Poliovirus type 3 (strain Saukett) stabilized virus-like particle in complex with the… · 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 5O5P · PDBe 5O5P · UniProt Q84895 · UniProt P03302
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