Research workbench
Crystal structure of H15 hemagglutinin from A/SHEARWATER/WA/2576/1979 H15N9 influenza virus in complex with 3'-sln
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
- 5TG9
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Hemagglutinin HA2 chain
- UniProt
- L0L3X3
- Ligands
- NAG, GAL, SIA
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin | protein | 325 | 9% helix, 39% strand | L0L3X3 |
| B, D | Hemagglutinin HA2 chain | protein | 168 | 53% helix, 14% strand | L0L3X3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.61 | 0.82 | 22 | empty |
| 2 | 208 | 0.60 | 0.81 | 22 | empty |
| 3 | 363 | 0.52 | 0.73 | 40 | empty |
| 4 | 212 | 0.47 | 0.75 | 26 | empty |
| 5 | 90 | 0.45 | 0.81 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3049 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3024 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5TG9 · 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 5TG9 · PDBe 5TG9 · UniProt L0L3X3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.