Research workbench
Structure of full-length influenza hemagglutinin with tilted transmembrane (A/DUCK/ALBERTA/35/76[H1N1])
Analyse Structure of full-length influenza hemagglutinin with tilted transmembrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HJR
- Type
- protein
- Length
- 1,578 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q9WCE0, P26562
- Ligands
- NAG, FUC, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 323 | 8% helix, 34% strand | Q9WCE0 |
| B, D, F | Hemagglutinin | protein | 203 | 54% helix, 6% strand | P26562 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C, D, E, F
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.83 | 0.86 | 94 | empty |
| 2 | 1046 | 0.83 | 0.84 | 104 | empty |
| 3 | 74 | 0.73 | 0.97 | 23 | empty |
| 4 | 703 | 0.72 | 0.79 | 48 | empty |
| 5 | 321 | 0.72 | 0.85 | 44 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2711 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2694 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2581 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 1421 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1366 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6HJR · Structure of full-length Influenza Hemagglutinin with tilted transmembrane… · 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 6HJR · PDBe 6HJR · UniProt Q9WCE0 · UniProt P26562
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