Research workbench
Poliovirus (type 1, mahoney strain) complexed with R78206
Analyse Poliovirus (type 1, mahoney strain) complexed with R78206 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VBD
- Type
- protein
- Length
- 851 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poliovirus type 1 mahoney
- UniProt
- P03300
- Ligands
- J78, MYR
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Poliovirus type 1 mahoney | protein | 5 | 0% helix, 0% strand | — |
| 1 | Poliovirus type 1 mahoney | protein | 283 | 8% helix, 31% strand | P03300 |
| 2 | Poliovirus type 1 mahoney | protein | 266 | 13% helix, 38% strand | P03300 |
| 3 | Poliovirus type 1 mahoney | protein | 235 | 10% helix, 30% strand | P03300 |
| 4 | Poliovirus type 1 mahoney | protein | 62 | 11% helix, 16% strand | — |
Ligands and binding sites
- J78 · (methylpyridazine piperidine propyloxyphenyl)ethylacetate · ligand · chains 1, 3
- MYR · Myristic acid · ligand · chains 0, 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.80 | 0.83 | 90 | J78 |
| 2 | 140 | 0.47 | 0.78 | 27 | empty |
| 3 | 77 | 0.42 | 0.80 | 17 | empty |
| 4 | 166 | 0.41 | 0.73 | 29 | empty |
| 5 | 83 | 0.39 | 0.77 | 17 | empty |
Interfaces
7 interfaces between chains.
- 1–3 · 3962 Ų buried · 76 hydrogen bonds · protein-protein
- 1–2 · 2423 Ų buried · 43 hydrogen bonds · protein-protein
- 2–3 · 1658 Ų buried · 22 hydrogen bonds · protein-protein
- 1–4 · 1182 Ų buried · 16 hydrogen bonds · protein-protein
- 3–4 · 858 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 1VBD · Poliovirus (type 1, mahoney strain) complexed with R78206 · 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 P03300
- Elsewhere: RCSB PDB 1VBD · PDBe 1VBD · UniProt P03300
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