Research workbench
Poliovirus (type 3, sabin strain) (P3/SABIN, P3/LEON/12A(1) B) complexed with R78206
Analyse Poliovirus (type 3, sabin strain) (P3/SABIN, P3/LEON/12A(1) B) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VBA
- 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
- MYR, J78
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 10% 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 | 13% helix, 38% strand | P03302 |
| 3 | Poliovirus type 3 | protein | 235 | 10% helix, 30% strand | P03302 |
| 4 | Poliovirus type 3 | protein | 62 | 11% helix, 15% strand | P03302 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains 4
- J78 · (methylpyridazine piperidine propyloxyphenyl)ethylacetate · ligand · chains 1, 3
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.81 | 0.85 | 80 | J78 |
| 2 | 71 | 0.65 | 0.93 | 22 | empty |
| 3 | 186 | 0.47 | 0.76 | 34 | empty |
| 4 | 145 | 0.46 | 0.77 | 31 | empty |
| 5 | 87 | 0.44 | 0.80 | 17 | empty |
Interfaces
7 interfaces between chains.
- 1–3 · 3964 Ų buried · 72 hydrogen bonds · protein-protein
- 1–2 · 2358 Ų buried · 38 hydrogen bonds · protein-protein
- 2–3 · 1704 Ų buried · 19 hydrogen bonds · protein-protein
- 1–4 · 913 Ų buried · 12 hydrogen bonds · protein-protein
- 3–4 · 879 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 1VBA · Poliovirus (type 3, sabin strain) (P3/SABIN, P3/LEON/12A(1)B) 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 1VBA · PDBe 1VBA · UniProt P03302
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