Research workbench
Puumala virus-like particle glycoprotein spike and lattice contacts model.
Analyse Puumala virus-like particle glycoprotein spike and lattice contacts model. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B0A
- Type
- protein
- Length
- 1,506 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope polyprotein
- UniProt
- Q9WJ31
- Ligands
- NAG, BMA, MAN
- Pockets
- 17 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Envelope polyprotein | protein | 422 | 3% helix, 52% strand | Q9WJ31 |
| B, G | Envelope polyprotein | protein | 331 | 11% helix, 47% strand | Q9WJ31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, D, G
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.75 | 0.79 | 111 | empty |
| 2 | 349 | 0.67 | 0.81 | 50 | empty |
| 3 | 387 | 0.63 | 0.78 | 50 | empty |
| 4 | 389 | 0.63 | 0.78 | 46 | empty |
| 5 | 352 | 0.61 | 0.78 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1320 Ų buried · 29 hydrogen bonds · protein-protein
- D–G · 1318 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 608 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7B0A · Puumala virus-like particle glycoprotein spike and lattice contacts model. · the same entry in another collection · chain A against A, 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 Q9WJ31
- Elsewhere: RCSB PDB 7B0A · PDBe 7B0A · UniProt Q9WJ31
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.