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Crystal structure of hemagglutinin of influenza virus B/YAMANASHI/166/1998
Analyse Crystal structure of hemagglutinin of influenza virus B/YAMANASHI/166/1998 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M40
- Type
- protein
- Length
- 1,541 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- A3DQM7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 343 | 7% helix, 35% strand | A3DQM7 |
| B, F | Hemagglutinin HA2 | protein | 171 | 51% helix, 11% strand | A3DQM7 |
| D | Hemagglutinin HA2 | protein | 170 | 52% helix, 11% strand | A3DQM7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.89 | 0.90 | 131 | empty |
| 2 | 1026 | 0.88 | 0.89 | 90 | empty |
| 3 | 98 | 0.79 | 0.99 | 16 | empty |
| 4 | 126 | 0.73 | 0.93 | 21 | empty |
| 5 | 50 | 0.69 | 0.97 | 21 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2998 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2992 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 2973 Ų buried · 51 hydrogen bonds · protein-protein
- B–F · 1616 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1610 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 4M40 · Crystal structure of hemagglutinin of influenza virus B/Yamanashi/166/1998 · 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 A3DQM7
- Elsewhere: RCSB PDB 4M40 · PDBe 4M40 · UniProt A3DQM7
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