Research workbench
Structure of H1 (A/SOLOMON ISLANDS/3/06) influenza hemagglutinin in complex with SD38
Analyse Structure of H1 (A/SOLOMON ISLANDS/3/06) influenza hemagglutinin in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FYT
- Type
- protein
- Length
- 619 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Single domain antibody SD38
- UniProt
- A7Y8I1
- Ligands
- NAG, FUC, BMA
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 322 | 8% helix, 41% strand | A7Y8I1 |
| B | Hemagglutinin | protein | 173 | 56% helix, 13% strand | A7Y8I1 |
| I | Single domain antibody SD38 | protein | 124 | 2% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, I
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.56 | 0.81 | 24 | empty |
| 2 | 154 | 0.53 | 0.80 | 21 | empty |
| 3 | 119 | 0.39 | 0.75 | 25 | empty |
| 4 | 72 | 0.36 | 0.77 | 16 | empty |
| 5 | 63 | 0.31 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2812 Ų buried · 42 hydrogen bonds · protein-protein
- B–I · 748 Ų buried · 5 hydrogen bonds · protein-protein
- A–I · 145 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 6FYT · Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38 · 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 A7Y8I1
- Elsewhere: RCSB PDB 6FYT · PDBe 6FYT · UniProt A7Y8I1
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