MolNFT v1 · #98890 · protein
The crystal structure of hemagglutinin form a H7N9 influenza virus (A/SHANGHAI/1/2013) in complex with lstb
4LN4: “The crystal structure of hemagglutinin form a H7N9 influenza virus (A/SHANGHAI/1/2013) in complex with lstb”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #98890 on GenesisL1: 3D structure…
- PDB
- 4LN4
- Type
- protein
- Length
- 2,889 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin | protein | 316 | 9% helix, 40% strand | — |
| B, D, F | Hemagglutinin | protein | 167 | 50% helix, 12% strand | — |
| H, J, L | Hemagglutinin | protein | 164 | 50% helix, 12% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.86 | 0.87 | 104 | empty |
| 2 | 177 | 0.82 | 0.97 | 26 | empty |
| 3 | 179 | 0.82 | 0.97 | 27 | empty |
| 4 | 178 | 0.82 | 0.97 | 28 | empty |
| 5 | 1039 | 0.78 | 0.80 | 112 | empty |
Interfaces
21 interfaces between chains.
- K–L · 3125 Ų buried · 44 hydrogen bonds · protein-protein
- I–J · 3101 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 3098 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3093 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 3083 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 4LN4 · The crystal structure of hemagglutinin form a h7n9 influenza virus (a/shanghai/1/2013) in… · 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 4LN4 · PDBe 4LN4
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