MolNFT v1 · #96792 · protein
Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E complexed with human receptor analogue lstc
4JU0: “Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E complexed with human receptor…”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 20 pockets (best druggability 0.84). MolNFT v1 #96792 on GenesisL1: 3D…
- PDB
- 4JU0
- Type
- protein
- Length
- 2,902 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C3W5S1
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Hemagglutinin | protein | 322 | 8% helix, 39% strand | C3W5S1 |
| B, H | Hemagglutinin | protein | 162 | 48% helix, 14% strand | C3W5S1 |
| C, E, I, K | Hemagglutinin | protein | 321 | 8% helix, 39% strand | C3W5S1 |
| D, J | Hemagglutinin | protein | 164 | 47% helix, 14% strand | C3W5S1 |
| F, L | Hemagglutinin | protein | 161 | 48% helix, 15% strand | C3W5S1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, C, E, G, I, K
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains A, C, E, G, I
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, C, E, G, I, K
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 | 212 | 0.84 | 0.97 | 25 | empty |
| 2 | 201 | 0.83 | 0.97 | 26 | empty |
| 3 | 1084 | 0.83 | 0.84 | 115 | empty |
| 4 | 123 | 0.78 | 0.96 | 34 | empty |
| 5 | 1178 | 0.78 | 0.80 | 86 | empty |
Interfaces
34 interfaces between chains.
- I–J · 2819 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2806 Ų buried · 37 hydrogen bonds · protein-protein
- K–L · 2796 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2776 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2772 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 4JU0 · Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E 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 C3W5S1
- Elsewhere: RCSB PDB 4JU0 · PDBe 4JU0 · UniProt C3W5S1
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