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Crystal structure of hemagglutinin of influenza virus B/YAMANASHI/166/1998 in complex with avian-like receptor lsta
Analyse Crystal structure of hemagglutinin of influenza virus B/YAMANASHI/166/1998 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M44
- 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, GAL, SIA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 24% 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, 12% strand | A3DQM7 |
| D | Hemagglutinin HA2 | protein | 170 | 51% helix, 12% strand | A3DQM7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
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 | 1025 | 0.87 | 0.89 | 90 | empty |
| 2 | 435 | 0.85 | 0.92 | 79 | empty |
| 3 | 208 | 0.80 | 0.93 | 37 | empty |
| 4 | 92 | 0.78 | 0.99 | 14 | empty |
| 5 | 104 | 0.70 | 0.92 | 25 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3006 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2994 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2994 Ų buried · 49 hydrogen bonds · protein-protein
- B–F · 1609 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1589 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 4M44 · Crystal structure of hemagglutinin of influenza virus B/Yamanashi/166/1998 in complex… · the same entry in another collection · chain E against E, 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 4M44 · PDBe 4M44 · UniProt A3DQM7
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