Research workbench
The structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6 influenza virus in complex with human receptor analog lstc
Analyse The structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XLD
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A3KF09
- Ligands
- NAG, GAL, SIA
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 319 | 9% helix, 39% strand | A3KF09 |
| C, D | Hemagglutinin | protein | 172 | 54% helix, 15% strand | A3KF09 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.58 | 0.80 | 34 | empty |
| 2 | 202 | 0.54 | 0.79 | 28 | empty |
| 3 | 160 | 0.50 | 0.78 | 24 | empty |
| 4 | 156 | 0.50 | 0.78 | 25 | empty |
| 5 | 101 | 0.45 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2979 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2971 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 212 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5XLD · The structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6 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 A3KF09
- Elsewhere: RCSB PDB 5XLD · PDBe 5XLD · UniProt A3KF09
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