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The crystal structure of hemagglutinin from A/HONG KONG/125/2017 H7N9 influenza virus
Analyse The crystal structure of hemagglutinin from A/HONG KONG/125/2017 H7N9 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D8B
- Type
- protein
- Length
- 1,461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- A0A2I7YV81, A0A218MY65
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 316 | 9% helix, 41% strand | A0A2I7YV81 |
| B, D, F | Hemagglutinin HA2 chain | protein | 171 | 54% helix, 12% strand | A0A218MY65 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, 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 | 225 | 0.84 | 0.97 | 25 | empty |
| 2 | 182 | 0.82 | 0.97 | 27 | empty |
| 3 | 334 | 0.82 | 0.92 | 31 | empty |
| 4 | 180 | 0.81 | 0.96 | 27 | empty |
| 5 | 179 | 0.81 | 0.96 | 26 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3171 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 3164 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3083 Ų buried · 48 hydrogen bonds · protein-protein
- D–F · 1507 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1499 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6D8B · The crystal structure of hemagglutinin from A/Hong Kong/125/2017 H7N9 influenza virus · 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 A0A2I7YV81
- Every structure of UniProt A0A218MY65
- Elsewhere: RCSB PDB 6D8B · PDBe 6D8B · UniProt A0A2I7YV81 · UniProt A0A218MY65
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