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The crystal structure of hemagglutinin from a H3N8 influenza virus isolated from new england harbor seals
Analyse The crystal structure of hemagglutinin from a H3N8 influenza virus isolated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WA1
- Type
- protein
- Length
- 2,946 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- I6NNE1
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hemagglutinin | protein | 491 | 25% helix, 32% strand | I6NNE1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, D, C, E, F
- BMA · beta-D-mannopyranose · sugar · 2 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.87 | 0.88 | 136 | empty |
| 2 | 251 | 0.84 | 0.96 | 31 | empty |
| 3 | 717 | 0.73 | 0.79 | 60 | empty |
| 4 | 933 | 0.72 | 0.76 | 75 | empty |
| 5 | 517 | 0.71 | 0.81 | 51 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2462 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2451 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 2409 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2375 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 4WA1 · The crystal structure of hemagglutinin from a H3N8 influenza virus isolated from New… · 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 I6NNE1
- Elsewhere: RCSB PDB 4WA1 · PDBe 4WA1 · UniProt I6NNE1
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