Research workbench
Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed with human receptor analogue lstc
Analyse Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JUJ
- Type
- protein
- Length
- 1,471 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q9WFX3
- Ligands
- NAG, GAL, SIA
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 324 | 10% helix, 37% strand | Q9WFX3 |
| B | Hemagglutinin | protein | 170 | 54% helix, 12% strand | Q9WFX3 |
| D | Hemagglutinin | protein | 164 | 51% helix, 11% strand | Q9WFX3 |
| F | Hemagglutinin | protein | 165 | 50% helix, 11% strand | Q9WFX3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, E
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.85 | 0.85 | 135 | empty |
| 2 | 108 | 0.78 | 0.97 | 15 | empty |
| 3 | 870 | 0.74 | 0.78 | 99 | empty |
| 4 | 787 | 0.73 | 0.78 | 68 | empty |
| 5 | 669 | 0.72 | 0.79 | 54 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2782 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2771 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2724 Ų buried · 45 hydrogen bonds · protein-protein
- D–F · 1180 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1145 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4JUJ · Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed… · 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 Q9WFX3
- Elsewhere: RCSB PDB 4JUJ · PDBe 4JUJ · UniProt Q9WFX3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.