MolNFT v1 · #96811 · protein
Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed with human receptor analogue lstc
4JUJ: “Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed with human receptor…”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 15 pockets (best druggability 0.85). MolNFT v1 #96811 on GenesisL1: 3D…
- 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
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