Research workbench
Complex of poliovirus with vhh PVSS21E
Analyse Complex of poliovirus with vhh PVSS21E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBG
- Type
- protein
- Length
- 974 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
- 13 · best druggability 0.73
Structure
electron microscopy · 5 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid protein VP1 | protein | 283 | 11% helix, 31% strand | P03300 |
| 2 | Capsid protein VP2 | protein | 267 | 13% helix, 38% strand | P03300 |
| 3 | Capsid protein VP3 | protein | 235 | 9% helix, 30% strand | P03300 |
| 4 | Capsid protein VP4 | protein | 68 | 10% helix, 15% strand | P03300 |
| 7 | Nanobody vhh PVSS21E | protein | 121 | 2% helix, 44% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.73 | 0.88 | 44 | PLM |
| 2 | 56 | 0.58 | 0.91 | 15 | empty |
| 3 | 88 | 0.56 | 0.86 | 23 | empty |
| 4 | 141 | 0.47 | 0.78 | 29 | empty |
| 5 | 170 | 0.41 | 0.73 | 22 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 3947 Ų buried · 62 hydrogen bonds · protein-protein
- 1–2 · 2383 Ų buried · 32 hydrogen bonds · protein-protein
- 2–3 · 1699 Ų buried · 19 hydrogen bonds · protein-protein
- 1–4 · 1201 Ų buried · 16 hydrogen bonds · protein-protein
- 3–4 · 883 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 lipid (disulfide, myristoylation).
Compared structures
- 3JBG · Complex of poliovirus with VHH PVSS21E · 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 3JBG · PDBe 3JBG · UniProt P03300
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