Research workbench
Complex of poliovirus with vhh PVSP19B
Analyse Complex of poliovirus with vhh PVSP19B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBF
- Type
- protein
- Length
- 976 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4; Nanobody…
- UniProt
- P03300
- Ligands
- MYR, PLM
- Pockets
- 11 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid protein VP1 | protein | 283 | 7% helix, 29% strand | P03300 |
| 2 | Capsid protein VP2 | protein | 267 | 11% helix, 34% strand | P03300 |
| 3 | Capsid protein VP3 | protein | 235 | 8% helix, 30% strand | P03300 |
| 4 | Capsid protein VP4 | protein | 68 | 6% helix, 9% strand | P03300 |
| 7 | Nanobody vhh PVSP19B | protein | 123 | 7% helix, 38% strand | — |
Ligands and binding sites
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 | 159 | 0.78 | 0.94 | 34 | PLM |
| 2 | 530 | 0.63 | 0.75 | 65 | empty |
| 3 | 157 | 0.50 | 0.78 | 29 | empty |
| 4 | 78 | 0.45 | 0.81 | 18 | empty |
| 5 | 162 | 0.41 | 0.73 | 22 | empty |
Interfaces
7 interfaces between chains.
- 1–3 · 3915 Ų buried · 63 hydrogen bonds · protein-protein
- 1–2 · 2392 Ų buried · 32 hydrogen bonds · protein-protein
- 2–3 · 1712 Ų buried · 18 hydrogen bonds · protein-protein
- 1–4 · 1233 Ų buried · 15 hydrogen bonds · protein-protein
- 3–4 · 851 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 lipid (disulfide, myristoylation).
Compared structures
- 3JBF · Complex of poliovirus with VHH PVSP19B · 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 3JBF · PDBe 3JBF · UniProt P03300
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