MolNFT v1 · #117362 · protein
Hemagglutinin-esterase-fusion mutant structure of influenza D virus
5E5W: “Hemagglutinin-esterase-fusion mutant structure of influenza D virus”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.54). MolNFT v1 #117362 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E5W
- Type
- protein
- Length
- 1,146 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase
- UniProt
- K9LG83
- Ligands
- NAG, MAN, BMA
- Pockets
- 10 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin-esterase | protein | 424 | 14% helix, 35% strand | K9LG83 |
| B, D | Hemagglutinin-esterase | protein | 149 | 47% helix, 13% strand | K9LG83 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, D, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.54 | 0.77 | 30 | NAG |
| 2 | 247 | 0.50 | 0.74 | 36 | empty |
| 3 | 115 | 0.45 | 0.78 | 24 | empty |
| 4 | 97 | 0.39 | 0.77 | 17 | empty |
| 5 | 127 | 0.37 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3321 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3265 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 674 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5E5W · Hemagglutinin-esterase-fusion mutant structure of influenza D virus · 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 K9LG83
- Elsewhere: RCSB PDB 5E5W · PDBe 5E5W · UniProt K9LG83
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