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Crystal structure of H5N1 influenza virus hemagglutinin, strain 437-10
Analyse Crystal structure of H5N1 influenza virus hemagglutinin, strain 437-10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S11
- Type
- protein
- Length
- 1,480 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q9EA62
- Ligands
- TAM, NAG, BMA
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemagglutinin HA1 chain | protein | 322 | 10% helix, 41% strand | Q9EA62 |
| B | Hemagglutinin HA2 chain | protein | 170 | 54% helix, 12% strand | Q9EA62 |
| C | Hemagglutinin HA1 chain | protein | 321 | 9% helix, 41% strand | Q9EA62 |
| D | Hemagglutinin HA2 chain | protein | 172 | 57% helix, 12% strand | Q9EA62 |
| F | Hemagglutinin HA2 chain | protein | 173 | 57% helix, 12% strand | Q9EA62 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.86 | 0.88 | 119 | empty |
| 2 | 60 | 0.74 | 0.99 | 15 | empty |
| 3 | 159 | 0.68 | 0.88 | 26 | empty |
| 4 | 449 | 0.67 | 0.79 | 56 | empty |
| 5 | 301 | 0.66 | 0.82 | 41 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2519 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2512 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2505 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 1394 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1356 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 3S11 · Crystal structure of H5N1 influenza virus hemagglutinin, strain 437-10 · 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 Q9EA62
- Elsewhere: RCSB PDB 3S11 · PDBe 3S11 · UniProt Q9EA62
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