Research workbench
The structure of hemagglutinin from avian-origin H7N9 influenza virus
Analyse The structure of hemagglutinin from avian-origin H7N9 influenza virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KOL
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 314 | 8% helix, 39% strand | — |
| B | Hemagglutinin HA2 | protein | 163 | 51% helix, 12% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.61 | 0.81 | 25 | empty |
| 2 | 73 | 0.45 | 0.81 | 18 | empty |
| 3 | 107 | 0.44 | 0.78 | 21 | empty |
| 4 | 61 | 0.44 | 0.82 | 15 | empty |
| 5 | 50 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3016 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4KOL · The structure of hemagglutinin from avian-origin H7N9 influenza virus · 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 4KOL · PDBe 4KOL
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