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The structure of hemagglutinin from a H6N1 influenza virus (A/TAIWAN/2/2013) in complex with human receptor analog 6'SLNLN
Analyse The structure of hemagglutinin from a H6N1 influenza virus (A/TAIWAN/2/2013) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YYB
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HA1; HA2
- Ligands
- NAG, GAL, SIA, BMA
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HA1 | protein | 325 | 9% helix, 39% strand | — |
| B | HA2 | protein | 162 | 52% helix, 14% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.61 | 0.88 | 20 | empty |
| 2 | 73 | 0.46 | 0.82 | 20 | empty |
| 3 | 92 | 0.43 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2692 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4YYB · The structure of hemagglutinin from a H6N1 influenza virus (A/Taiwan/2/2013) in complex… · 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
- Elsewhere: RCSB PDB 4YYB · PDBe 4YYB
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