Research workbench
Complex structure of H4 hemagglutinin from avian influenza H4N6 virus with lsta
Analyse Complex structure of H4 hemagglutinin from avian influenza H4N6 virus with lsta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XL3
- 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, SIA, GAL
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 319 | 8% helix, 40% strand | A3KF09 |
| C, D | Hemagglutinin | protein | 172 | 52% helix, 15% strand | A3KF09 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · chains B
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 | 216 | 0.57 | 0.79 | 30 | empty |
| 2 | 227 | 0.56 | 0.79 | 32 | empty |
| 3 | 181 | 0.48 | 0.76 | 27 | empty |
| 4 | 105 | 0.45 | 0.79 | 25 | empty |
| 5 | 74 | 0.39 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2965 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 2951 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 223 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5XL3 · Complex structure of H4 hemagglutinin from avian influenza H4N6 virus with LSTa · 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 5XL3 · PDBe 5XL3 · UniProt A3KF09
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