MolNFT v1 · #119520 · protein
Sub-tomogram averaging of tula virus glycoprotein spike
5FYN · Puumala virus gn glycoprotein: “Sub-tomogram averaging of tula virus glycoprotein spike”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.63). MolNFT v1 #119520 on GenesisL1: 3D structure, binding…
- PDB
- 5FYN
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Puumala virus gn glycoprotein
- UniProt
- Q9WJ31
- Ligands
- NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.63
Structure
electron microscopy · 2 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Puumala virus gn glycoprotein | protein | 331 | 11% helix, 47% strand | Q9WJ31 |
| B | Puumala virus gn glycoprotein | protein | 332 | 11% helix, 46% strand | Q9WJ31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.63 | 0.80 | 41 | empty |
| 2 | 356 | 0.62 | 0.78 | 40 | empty |
| 3 | 339 | 0.62 | 0.79 | 36 | empty |
| 4 | 299 | 0.57 | 0.77 | 38 | empty |
| 5 | 161 | 0.49 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5FYN · Sub-tomogram averaging of Tula virus glycoprotein spike · 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 5FYN · PDBe 5FYN · UniProt Q9WJ31
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