Research workbench
1930 swine H1 hemagglutinin
Analyse 1930 swine H1 hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RUY
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q82500, P88836
- Ligands
- NDG, NAG
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J, L | Hemagglutinin | protein | 324 | 9% helix, 41% strand | Q82500 |
| I, K, M | Hemagglutinin | protein | 160 | 51% helix, 14% strand | P88836 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 5 copies · chains H, J, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.88 | 0.91 | 134 | empty |
| 2 | 577 | 0.70 | 0.79 | 46 | empty |
| 3 | 563 | 0.69 | 0.78 | 46 | empty |
| 4 | 528 | 0.68 | 0.78 | 38 | empty |
| 5 | 215 | 0.60 | 0.81 | 38 | empty |
Interfaces
15 interfaces between chains.
- J–K · 2715 Ų buried · 44 hydrogen bonds · protein-protein
- H–I · 2712 Ų buried · 44 hydrogen bonds · protein-protein
- L–M · 2711 Ų buried · 44 hydrogen bonds · protein-protein
- I–M · 1106 Ų buried · 10 hydrogen bonds · protein-protein
- K–M · 1082 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1RUY · 1930 Swine H1 Hemagglutinin · the same entry in another collection · chain H against H, 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 Q82500
- Every structure of UniProt P88836
- Elsewhere: RCSB PDB 1RUY · PDBe 1RUY · UniProt Q82500 · UniProt P88836
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