Research workbench
Binding of influenza virus hemagglutinin to analogs of its cell- surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography
Analyse Binding of influenza virus hemagglutinin to analogs of its cell- surface… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HGG
- Type
- protein
- Length
- 1,509 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin, chain HA1; Hemagglutinin, chain HA2
- UniProt
- P03437
- Ligands
- NAG, BGC, GAL, SIA, BMA
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin, chain HA1 | protein | 328 | 9% helix, 41% strand | P03437 |
| B, D, F | Hemagglutinin, chain HA2 | protein | 175 | 54% helix, 15% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, E, C, B, D, F
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains E, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.87 | 0.88 | 97 | empty |
| 2 | 284 | 0.84 | 0.95 | 31 | empty |
| 3 | 747 | 0.75 | 0.80 | 82 | BGC, GAL, SIA |
| 4 | 89 | 0.74 | 0.97 | 21 | empty |
| 5 | 700 | 0.74 | 0.80 | 71 | BGC, GAL, SIA |
Interfaces
15 interfaces between chains.
- E–F · 3152 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3133 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 3025 Ų buried · 50 hydrogen bonds · protein-protein
- B–F · 1593 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1577 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 1HGG · Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic… · 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 P03437
- Elsewhere: RCSB PDB 1HGG · PDBe 1HGG · UniProt P03437
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