Research workbench
Crystal structure of H15 hemagglutinin from A/SHEARWATER/WA/2576/1979 H15N9 influenza virus
Analyse Crystal structure of H15 hemagglutinin from A/SHEARWATER/WA/2576/1979 H15N9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TG8
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- L0L3X3
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin HA1 chain | protein | 328 | 8% helix, 37% strand | L0L3X3 |
| B, D | Hemagglutinin HA2 chain | protein | 169 | 47% helix, 15% strand | L0L3X3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.64 | 0.74 | 67 | NAG |
| 2 | 206 | 0.60 | 0.81 | 22 | empty |
| 3 | 200 | 0.60 | 0.81 | 22 | empty |
| 4 | 93 | 0.44 | 0.80 | 19 | empty |
| 5 | 105 | 0.44 | 0.78 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3066 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 3047 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 285 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 76 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5TG8 · Crystal structure of H15 hemagglutinin from A/shearwater/WA/2576/1979 H15N9 influenza… · 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 L0L3X3
- Elsewhere: RCSB PDB 5TG8 · PDBe 5TG8 · UniProt L0L3X3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.