MolNFT v1 · #119494 · protein
Crystal structure of puumala virus gn glycoprotein ectodomain
5FXU · Envelope polyprotein: “Crystal structure of puumala virus gn glycoprotein ectodomain”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 7 pockets (best druggability 0.68). MolNFT v1 #119494 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5FXU
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope polyprotein
- UniProt
- Q9WJ31
- Ligands
- NAG, BMA, MAN
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope polyprotein | protein | 331 | 11% helix, 47% strand | Q9WJ31 |
| B | Envelope polyprotein | 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.68 | 0.77 | 49 | empty |
| 2 | 309 | 0.61 | 0.79 | 44 | empty |
| 3 | 364 | 0.61 | 0.77 | 40 | empty |
| 4 | 339 | 0.60 | 0.78 | 39 | empty |
| 5 | 142 | 0.49 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 217 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5FXU · Crystal Structure of Puumala virus Gn glycoprotein ectodomain · 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 5FXU · PDBe 5FXU · UniProt Q9WJ31
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