MolNFT v1 · #111678 · protein
The structure of hemagglutinin from a H6N1 influenza virus (A/CHICKEN/TAIWAN/A2837/2013)
4YY0 · HA1: “The structure of hemagglutinin from a H6N1 influenza virus (A/CHICKEN/TAIWAN/A2837/2013)”. X-ray diffraction, 1 ligand (NAG), 16 pockets (best druggability 0.87). MolNFT v1 #111678 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YY0
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HA1; HA2
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | HA1 | protein | 325 | 10% helix, 39% strand | — |
| B, D, F | HA2 | protein | 159 | 47% helix, 12% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.87 | 0.88 | 126 | empty |
| 2 | 90 | 0.78 | 0.98 | 17 | empty |
| 3 | 971 | 0.75 | 0.78 | 85 | empty |
| 4 | 848 | 0.71 | 0.77 | 92 | empty |
| 5 | 315 | 0.65 | 0.81 | 45 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2773 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2696 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 2662 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 1274 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1240 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 4YY0 · 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 4YY0 · PDBe 4YY0
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