MolNFT v1 · #57863 · protein
Crystal structure of the swine-origin a (H1N1)-2009 influenza a virus hemagglutinin (ha) reveals similar antigenicity to that of the 1918 pandemic virus
3AL4: “Crystal structure of the swine-origin a (H1N1)-2009 influenza a virus hemagglutinin (ha) reveals similar…”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #57863 on GenesisL1: 3D structure…
- PDB
- 3AL4
- Type
- protein
- Length
- 2,896 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C3W5S1
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin | protein | 321 | 8% helix, 37% strand | C3W5S1 |
| B, D, H, J | Hemagglutinin | protein | 162 | 48% helix, 15% strand | C3W5S1 |
| F, L | Hemagglutinin | protein | 161 | 49% helix, 14% strand | C3W5S1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, K, C, F, E, I, L, G
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.85 | 0.97 | 30 | empty |
| 2 | 224 | 0.84 | 0.96 | 28 | empty |
| 3 | 1143 | 0.83 | 0.84 | 132 | empty |
| 4 | 603 | 0.79 | 0.84 | 74 | empty |
| 5 | 121 | 0.78 | 0.96 | 23 | empty |
Interfaces
34 interfaces between chains.
- I–J · 2764 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2758 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2738 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2729 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2707 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 23 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 3AL4 · Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA)… · 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 C3W5S1
- Elsewhere: RCSB PDB 3AL4 · PDBe 3AL4 · UniProt C3W5S1
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