MolNFT v1 · #100701 · protein
Crystal structure of hemagglutinin from an H7N9 influenza virus
4N5J · Hemagglutinin HA1: “Crystal structure of hemagglutinin from an H7N9 influenza virus”. X-ray diffraction, 2 ligands (NAG, BMA), 11 pockets (best druggability 0.64). MolNFT v1 #100701 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4N5J
- Type
- protein
- Length
- 965 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- R4NN21
- Ligands
- NAG, BMA
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 318 | 8% helix, 39% strand | R4NN21 |
| B | Hemagglutinin HA2 | protein | 169 | 56% helix, 14% strand | R4NN21 |
| C | Hemagglutinin HA1 | protein | 317 | 8% helix, 36% strand | R4NN21 |
| D | Hemagglutinin HA2 | protein | 161 | 55% helix, 14% strand | R4NN21 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.64 | 0.82 | 25 | empty |
| 2 | 223 | 0.62 | 0.82 | 25 | empty |
| 3 | 113 | 0.50 | 0.81 | 24 | empty |
| 4 | 133 | 0.48 | 0.79 | 26 | empty |
| 5 | 75 | 0.47 | 0.83 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3147 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3068 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 262 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4N5J · Crystal structure of hemagglutinin from an H7N9 influenza virus · 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 R4NN21
- Elsewhere: RCSB PDB 4N5J · PDBe 4N5J · UniProt R4NN21
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