Research workbench
The structure of hemagglutinin from a H6N1 influenza virus (A/CHICKEN/TAIWAN/A2837/2013) in complex with avian receptor analog 3'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
- 4YY7
- 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 0.67
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HA1 | protein | 325 | 10% helix, 40% strand | — |
| B, D | HA2 | protein | 164 | 54% helix, 14% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.67 | 0.75 | 69 | empty |
| 2 | 110 | 0.43 | 0.77 | 19 | empty |
| 3 | 125 | 0.41 | 0.75 | 18 | empty |
| 4 | 66 | 0.29 | 0.73 | 21 | SIA |
Interfaces
3 interfaces between chains.
- C–D · 2762 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2757 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4YY7 · 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 4YY7 · PDBe 4YY7
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