MolNFT v1 · #159365 · protein
Crystal structure of influenza hemagglutinin from strain A/HICKOX/JY2/1940
6ONA: “Crystal structure of influenza hemagglutinin from strain A/HICKOX/JY2/1940”. X-ray diffraction, 3 ligands (NAG, BMA, CL), 12 pockets (best druggability 0.85). MolNFT v1 #159365 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6ONA
- Type
- protein
- Length
- 1,444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q0HD60, M1E1E4
- Ligands
- NAG, BMA, CL
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 479 | 23% helix, 33% strand | Q0HD60, M1E1E4 |
| B | Hemagglutinin | protein | 480 | 23% helix, 33% strand | Q0HD60, M1E1E4 |
| C | Hemagglutinin | protein | 485 | 23% helix, 33% strand | Q0HD60, M1E1E4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CL · Chloride ion · ion · 7 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.85 | 0.96 | 40 | CL |
| 2 | 895 | 0.82 | 0.84 | 140 | CL, PEG |
| 3 | 260 | 0.75 | 0.89 | 45 | empty |
| 4 | 247 | 0.74 | 0.88 | 41 | empty |
| 5 | 270 | 0.73 | 0.87 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2286 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2260 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2253 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6ONA · Crystal structure of Influenza hemagglutinin from strain A/Hickox/JY2/1940 · 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 Q0HD60
- Every structure of UniProt M1E1E4
- Elsewhere: RCSB PDB 6ONA · PDBe 6ONA · UniProt Q0HD60 · UniProt M1E1E4
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