MolNFT v1 · #151297 · protein
Structure of influenza hemagglutinin ectodomain (A/DUCK/ALBERTA/35/76)
6HJN: “Structure of influenza hemagglutinin ectodomain (A/DUCK/ALBERTA/35/76)”. Electron microscopy, 5 ligands (UPL, NAG, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #151297 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6HJN
- Type
- protein
- Length
- 1,488 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q9WCE0, P26562
- Ligands
- UPL, NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 23% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 323 | 7% helix, 34% strand | Q9WCE0 |
| B, D, F | Hemagglutinin | protein | 173 | 53% helix, 8% strand | P26562 |
Ligands and binding sites
- UPL · Unknown branched fragment of phospholipid · ligand · 3 copies · chains A, B, D, C, F, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, D, F, C, E
- BMA · beta-D-mannopyranose · sugar · 6 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.86 | 0.95 | 61 | empty |
| 2 | 661 | 0.80 | 0.85 | 91 | empty |
| 3 | 469 | 0.80 | 0.87 | 64 | empty |
| 4 | 775 | 0.74 | 0.79 | 55 | empty |
| 5 | 751 | 0.73 | 0.79 | 54 | empty |
Interfaces
15 interfaces between chains.
- F–E · 2727 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2724 Ų buried · 30 hydrogen bonds · protein-protein
- D–C · 2721 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 1142 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1140 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6HJN · Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76) · 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 6HJN · PDBe 6HJN · UniProt Q9WCE0 · UniProt P26562
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