Research workbench
Structure of an avian influenza H5 hemagglutinin from the influenza virus A/DUCK/EASTERN CHINA/L0230/2010 (H5N2)
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
- 7DEB
- Type
- protein
- Length
- 1,482 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A0A0X7YU24
- Ligands
- NAG, BMA
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin | protein | 494 | 23% helix, 31% strand | A0A0X7YU24 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.84 | 0.89 | 78 | empty |
| 2 | 157 | 0.83 | 0.99 | 16 | empty |
| 3 | 219 | 0.81 | 0.94 | 27 | empty |
| 4 | 220 | 0.81 | 0.94 | 27 | empty |
| 5 | 233 | 0.80 | 0.93 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2539 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2508 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2402 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7DEB · Structure of an avian influenza H5 hemagglutinin from the influenza virus A/duck/Eastern… · 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 A0A0X7YU24
- Elsewhere: RCSB PDB 7DEB · PDBe 7DEB · UniProt A0A0X7YU24
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