MolNFT v1 · #24955 · protein
Poliovirus (type 3, sabin strain, mutant 242-H2) complexed with R78206
1VBE · Poliovirus type 3: “Poliovirus (type 3, sabin strain, mutant 242-H2) complexed with R78206”. X-ray diffraction, 2 ligands (J78, MYR), 15 pockets (best druggability 0.80). MolNFT v1 #24955 on GenesisL1: 3D structure, binding sites…
- PDB
- 1VBE
- Type
- protein
- Length
- 846 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poliovirus type 3
- UniProt
- P03302
- Ligands
- J78, MYR
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Poliovirus type 3 | protein | 4 | 0% helix, 50% strand | — |
| 1 | Poliovirus type 3 | protein | 279 | 9% helix, 32% strand | P03302 |
| 2 | Poliovirus type 3 | protein | 266 | 14% helix, 38% strand | P03302 |
| 3 | Poliovirus type 3 | protein | 235 | 9% helix, 30% strand | P03302 |
| 4 | Poliovirus type 3 | protein | 62 | 11% helix, 15% strand | P03302 |
Ligands and binding sites
- J78 · (methylpyridazine piperidine propyloxyphenyl)ethylacetate · ligand · chains 1, 3
- MYR · Myristic acid · ligand · chains 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.80 | 0.84 | 92 | J78 |
| 2 | 70 | 0.65 | 0.93 | 19 | empty |
| 3 | 218 | 0.48 | 0.75 | 43 | empty |
| 4 | 144 | 0.46 | 0.77 | 33 | empty |
| 5 | 68 | 0.43 | 0.81 | 16 | empty |
Interfaces
7 interfaces between chains.
- 1–3 · 3964 Ų buried · 76 hydrogen bonds · protein-protein
- 1–2 · 2364 Ų buried · 42 hydrogen bonds · protein-protein
- 2–3 · 1689 Ų buried · 18 hydrogen bonds · protein-protein
- 1–4 · 919 Ų buried · 11 hydrogen bonds · protein-protein
- 3–4 · 882 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 1VBE · Poliovirus (type 3, sabin strain, mutant 242-H2) complexed with R78206 · 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 P03302
- Elsewhere: RCSB PDB 1VBE · PDBe 1VBE · UniProt P03302
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