Research workbench
Crystal structure of influenza hemagglutinin from strain A/MELBOURNE/1/1946(H1N1)
Analyse Crystal structure of influenza hemagglutinin from strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OSR
- Type
- protein
- Length
- 2,870 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C7S1Y2
- Ligands
- NAG, BMA, MAN, NA, K
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 481 | 24% helix, 32% strand | C7S1Y2 |
| B | Hemagglutinin | protein | 477 | 25% helix, 33% strand | C7S1Y2 |
| C | Hemagglutinin | protein | 476 | 24% helix, 31% strand | C7S1Y2 |
| D | Hemagglutinin | protein | 483 | 23% helix, 33% strand | C7S1Y2 |
| E | Hemagglutinin | protein | 477 | 23% helix, 31% strand | C7S1Y2 |
| F | Hemagglutinin | protein | 476 | 23% helix, 32% strand | C7S1Y2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains B, A, C, D, E, F
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- NA · Sodium ion · metal · 3 copies · chains C, E, F
- K · Potassium ion · metal · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, D, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.84 | 0.91 | 68 | empty |
| 2 | 208 | 0.83 | 0.96 | 21 | empty |
| 3 | 647 | 0.78 | 0.83 | 68 | empty |
| 4 | 575 | 0.77 | 0.83 | 57 | empty |
| 5 | 974 | 0.75 | 0.78 | 93 | EDO, NA |
Interfaces
7 interfaces between chains.
- D–E · 2067 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2066 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 2044 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2026 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2024 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 6OSR · Crystal structure of Influenza hemagglutinin from strain A/Melbourne/1/1946(H1N1) · 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 C7S1Y2
- Elsewhere: RCSB PDB 6OSR · PDBe 6OSR · UniProt C7S1Y2
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