Research workbench
Complex of poliovirus with vhh PVSP29F
Analyse Complex of poliovirus with vhh PVSP29F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBC
- Type
- protein
- Length
- 982 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
- 12 · best druggability 0.76
Structure
electron microscopy · 5 distinct chains · 10% helix, 32% 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 | 12% helix, 36% strand | P03300 |
| 3 | Capsid protein VP3 | protein | 235 | 9% helix, 31% strand | P03300 |
| 4 | Capsid protein VP4 | protein | 68 | 10% helix, 18% strand | P03300 |
| 7 | Nanobody vhh PVSP29F | protein | 129 | 5% helix, 36% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.76 | 0.88 | 41 | PLM |
| 2 | 606 | 0.71 | 0.79 | 63 | empty |
| 3 | 105 | 0.54 | 0.84 | 23 | empty |
| 4 | 130 | 0.43 | 0.76 | 25 | empty |
| 5 | 112 | 0.41 | 0.76 | 19 | empty |
Interfaces
8 interfaces between chains.
- 1–3 · 3921 Ų buried · 69 hydrogen bonds · protein-protein
- 1–2 · 2390 Ų buried · 35 hydrogen bonds · protein-protein
- 2–3 · 1702 Ų buried · 18 hydrogen bonds · protein-protein
- 1–4 · 1242 Ų buried · 22 hydrogen bonds · protein-protein
- 3–4 · 880 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 lipid (disulfide, myristoylation).
Compared structures
- 3JBC · Complex of Poliovirus with VHH PVSP29F · 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 3JBC · PDBe 3JBC · UniProt P03300
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