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Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E complexed with human receptor analogue lstc
Analyse Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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