Research workbench
Structure of an avian influenza H5 hemagglutinin from the influenza virus A/DUCK northern CHINA/22/2017 (H5N6)
Analyse Structure of an avian influenza H5 hemagglutinin from the influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DEA
- Type
- protein
- Length
- 1,470 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A0A6M2RI35
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, C | Hemagglutinin | protein | 319 | 9% helix, 41% strand | — |
| F, D, B | Hemagglutinin | protein | 171 | 57% helix, 13% strand | A0A6M2RI35 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains E, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.83 | 0.90 | 62 | empty |
| 2 | 453 | 0.79 | 0.87 | 58 | empty |
| 3 | 53 | 0.71 | 0.98 | 15 | empty |
| 4 | 312 | 0.65 | 0.81 | 42 | empty |
| 5 | 283 | 0.62 | 0.80 | 49 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2482 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2474 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2432 Ų buried · 28 hydrogen bonds · protein-protein
- D–B · 1292 Ų buried · 10 hydrogen bonds · protein-protein
- F–D · 1292 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7DEA · Structure of an avian influenza H5 hemagglutinin from the influenza virus A/duck Northern… · 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 A0A6M2RI35
- Elsewhere: RCSB PDB 7DEA · PDBe 7DEA · UniProt A0A6M2RI35
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.