Research workbench
Structure of influenza hemagglutinin ectodomain (A/DUCK/ALBERTA/35/76) in complex with FISW84 Fab fragment
Analyse Structure of influenza hemagglutinin ectodomain (A/DUCK/ALBERTA/35/76) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HJP
- Type
- protein
- Length
- 2,784 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Heavy chain of FISW84 Fab fragment; Light chain of FISW84 Fab fragment
- UniProt
- Q9WCE0, P26562
- Ligands
- UPL, NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 324 | 8% helix, 34% strand | Q9WCE0 |
| B, D, F | Hemagglutinin | protein | 174 | 57% helix, 6% strand | P26562 |
| G, I, K | Heavy chain of FISW84 Fab fragment | protein | 216 | 4% helix, 49% strand | — |
| H, J, L | Light chain of FISW84 Fab fragment | protein | 214 | 6% helix, 49% strand | — |
Ligands and binding sites
- UPL · Unknown branched fragment of phospholipid · ligand · 3 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 9 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.87 | 0.93 | 88 | empty |
| 2 | 357 | 0.79 | 0.89 | 55 | empty |
| 3 | 775 | 0.76 | 0.81 | 76 | empty |
| 4 | 344 | 0.76 | 0.87 | 54 | empty |
| 5 | 507 | 0.76 | 0.84 | 67 | empty |
Interfaces
30 interfaces between chains.
- C–D · 2737 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2730 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2725 Ų buried · 32 hydrogen bonds · protein-protein
- K–L · 1788 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 1731 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6HJP · Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76) in complex with… · 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 Q9WCE0
- Every structure of UniProt P26562
- Elsewhere: RCSB PDB 6HJP · PDBe 6HJP · UniProt Q9WCE0 · UniProt P26562
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