Research workbench
Structure of H1 1918 hemagglutinin with human receptor
Analyse Structure of H1 1918 hemagglutinin with human receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WRG
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q9WFX3
- Ligands
- NAG, GAL, SIA
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J, L | Hemagglutinin HA1 chain | protein | 324 | 8% helix, 37% strand | Q9WFX3 |
| I, K, M | Hemagglutinin HA2 chain | protein | 160 | 51% helix, 12% strand | Q9WFX3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains J, H, K, L, M
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains J
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.84 | 0.85 | 137 | empty |
| 2 | 175 | 0.82 | 0.96 | 24 | empty |
| 3 | 249 | 0.72 | 0.87 | 36 | empty |
| 4 | 378 | 0.70 | 0.82 | 58 | empty |
| 5 | 386 | 0.70 | 0.82 | 61 | empty |
Interfaces
15 interfaces between chains.
- H–I · 2750 Ų buried · 39 hydrogen bonds · protein-protein
- L–M · 2717 Ų buried · 39 hydrogen bonds · protein-protein
- J–K · 2711 Ų buried · 43 hydrogen bonds · protein-protein
- K–M · 1355 Ų buried · 15 hydrogen bonds · protein-protein
- I–K · 1350 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2WRG · structure of H1 1918 hemagglutinin with human receptor · the same entry in another collection · chain K against K, 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 2WRG · PDBe 2WRG · UniProt Q9WFX3
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