MolNFT v1 · #98892 · protein
The crystal structure of hemagglutinin from a H7N9 influenza virus (A/SHANGHAI/2/2013)
4LN6: “The crystal structure of hemagglutinin from a H7N9 influenza virus (A/SHANGHAI/2/2013)”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 20 pockets (best druggability 0.83). MolNFT v1 #98892 on GenesisL1: 3D structure, binding sites…
- PDB
- 4LN6
- Type
- protein
- Length
- 2,904 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, BMA, FUC, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin | protein | 316 | 9% helix, 39% strand | — |
| B, D, F | Hemagglutinin | protein | 167 | 56% helix, 13% strand | — |
| H, J, L | Hemagglutinin | protein | 169 | 55% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D, E, G, F, H, I, J, K, L
- BMA · beta-D-mannopyranose · sugar · 5 copies
- FUC · alpha-L-fucopyranose · sugar · chains G
- CA · Calcium ion · metal · 6 copies · chains A, C, E, G, I, K
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 | 398 | 0.83 | 0.91 | 36 | empty |
| 2 | 169 | 0.81 | 0.97 | 27 | empty |
| 3 | 171 | 0.81 | 0.96 | 27 | empty |
| 4 | 161 | 0.81 | 0.97 | 25 | empty |
| 5 | 166 | 0.81 | 0.96 | 26 | empty |
Interfaces
24 interfaces between chains.
- E–F · 3141 Ų buried · 43 hydrogen bonds · protein-protein
- I–J · 3137 Ų buried · 47 hydrogen bonds · protein-protein
- G–H · 3131 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 3130 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3128 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 4LN6 · The crystal structure of hemagglutinin from a h7n9 influenza virus (a/shanghai/2/2013) · 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 4LN6 · PDBe 4LN6
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