Research workbench
Crystal structure of the 1918 human H1 hemagglutinin precursor (HA0)
Analyse Crystal structure of the 1918 human H1 hemagglutinin precursor (HA0) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RD8
- Type
- protein
- Length
- 1,509 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, BMA, MAN, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 328 | 8% helix, 38% strand | — |
| B, D, F | Hemagglutinin | protein | 175 | 55% helix, 14% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, E, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar
- PO4 · Phosphate ion · ion · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.87 | 0.88 | 69 | empty |
| 2 | 259 | 0.85 | 0.96 | 30 | empty |
| 3 | 1126 | 0.85 | 0.86 | 86 | PO4 |
| 4 | 142 | 0.75 | 0.93 | 24 | empty |
| 5 | 145 | 0.73 | 0.92 | 26 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3055 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3054 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3043 Ų buried · 55 hydrogen bonds · protein-protein
- B–F · 1569 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1563 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 1RD8 · Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0) · 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
- Elsewhere: RCSB PDB 1RD8 · PDBe 1RD8
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