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The complex structure of hemagglutinin-esterase-fusion mutant protein from the influenza D virus with receptor analog 9-O-ac-3'SLN (TR322)
Analyse The complex structure of hemagglutinin-esterase-fusion mutant protein from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E65
- 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
- 5N6, NAG, MAN, BMA, GAL
- Pockets
- 9 · best druggability 0.56
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 | 48% helix, 12% strand | K9LG83 |
Ligands and binding sites
- 5N6 · 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid · ligand · 2 copies · chains A, C
- 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 · 3 copies · chains A, C
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.56 | 0.78 | 30 | empty |
| 2 | 298 | 0.52 | 0.74 | 36 | empty |
| 3 | 90 | 0.41 | 0.79 | 23 | empty |
| 4 | 93 | 0.37 | 0.76 | 16 | empty |
| 5 | 57 | 0.36 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3319 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 3288 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 651 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5E65 · The complex structure of Hemagglutinin-esterase-fusion mutant protein from the influenza… · 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 5E65 · PDBe 5E65 · UniProt K9LG83
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