Research workbench
Complex of poliovirus with vhh PVSP6A
Analyse Complex of poliovirus with vhh PVSP6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBD
- Type
- protein
- Length
- 973 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 0.78
Structure
electron microscopy · 5 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid protein VP1 | protein | 283 | 8% helix, 31% strand | P03300 |
| 2 | Capsid protein VP2 | protein | 267 | 12% helix, 35% strand | P03300 |
| 3 | Capsid protein VP3 | protein | 235 | 8% helix, 31% strand | P03300 |
| 4 | Capsid protein VP4 | protein | 68 | 10% helix, 15% strand | P03300 |
| 7 | Nanobody vhh PVSP6A | protein | 120 | 0% helix, 43% 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.78 | 0.84 | 74 | PLM |
| 2 | 606 | 0.62 | 0.74 | 49 | empty |
| 3 | 136 | 0.44 | 0.77 | 29 | empty |
| 4 | 54 | 0.44 | 0.84 | 16 | empty |
| 5 | 102 | 0.40 | 0.76 | 22 | empty |
Interfaces
8 interfaces between chains.
- 1–3 · 3947 Ų buried · 61 hydrogen bonds · protein-protein
- 1–2 · 2383 Ų buried · 29 hydrogen bonds · protein-protein
- 2–3 · 1729 Ų buried · 21 hydrogen bonds · protein-protein
- 1–4 · 1210 Ų buried · 17 hydrogen bonds · protein-protein
- 3–4 · 867 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 lipid (disulfide, myristoylation).
Compared structures
- 3JBD · Complex of poliovirus with VHH PVSP6A · 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 3JBD · PDBe 3JBD · UniProt P03300
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