MolNFT v1 · #157465 · protein
Crystal structure of hemagglutinin from influenza virus A/NETHERLANDS/209/1980 (H3N2)
6N08: “Crystal structure of hemagglutinin from influenza virus A/NETHERLANDS/209/1980 (H3N2)”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #157465 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6N08
- Type
- protein
- Length
- 1,464 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- H9XIV6
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin | protein | 488 | 25% helix, 32% strand | H9XIV6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.83 | 0.84 | 92 | empty |
| 2 | 96 | 0.74 | 0.96 | 22 | empty |
| 3 | 510 | 0.73 | 0.82 | 54 | empty |
| 4 | 87 | 0.72 | 0.95 | 22 | empty |
| 5 | 595 | 0.70 | 0.79 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2383 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2326 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2288 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 6N08 · Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2) · 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 H9XIV6
- Elsewhere: RCSB PDB 6N08 · PDBe 6N08 · UniProt H9XIV6
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