Research workbench
The structure of hemagglutinin from a H6N1 influenza virus (A/CHICKEN/TAIWAN/A2837/2013) in complex with human receptor analog 6'SLNLN
Analyse The structure of hemagglutinin from a H6N1 influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YY1
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HA1; HA2
- Ligands
- NAG, GAL, SIA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HA1 | protein | 325 | 9% helix, 40% strand | — |
| B, D | HA2 | protein | 164 | 51% helix, 12% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.66 | 0.80 | 41 | empty |
| 2 | 305 | 0.64 | 0.80 | 38 | empty |
| 3 | 50 | 0.32 | 0.77 | 16 | empty |
| 4 | 52 | 0.28 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2769 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2751 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 616 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4YY1 · The structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013)… · 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 4YY1 · PDBe 4YY1
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