Research workbench
The structure of hemagglutinin from avian-origin H7N9 influenza virus in complex with avian receptor analog 3'SLNLN (NEUACα2- 3GALβ1-4GLCNACβ1-3GALβ1-4GLC)
Analyse The structure of hemagglutinin from avian-origin H7N9 influenza virus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KOM
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- Ligands
- NAG, GAL, SIA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 314 | 9% helix, 39% strand | — |
| B | Hemagglutinin HA2 | protein | 166 | 50% helix, 12% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
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 | 242 | 0.65 | 0.83 | 25 | empty |
| 2 | 127 | 0.46 | 0.78 | 21 | empty |
| 3 | 61 | 0.39 | 0.80 | 16 | empty |
| 4 | 64 | 0.30 | 0.74 | 19 | SIA |
Interfaces
1 interface between chains.
- A–B · 3032 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4KOM · The structure of hemagglutinin from avian-origin H7N9 influenza virus in complex with… · 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 4KOM · PDBe 4KOM
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