Research workbench
The structure of hemagglutinin from a avian-origin H7N9 influenza virus (A/SHANGHAI/1/2013) in complex with avian receptor analog 3'SLNLN
Analyse The structure of hemagglutinin from a avian-origin H7N9 influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LKG
- Type
- protein
- Length
- 1,458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, GAL, SIA
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 316 | 9% helix, 39% strand | — |
| B, D, F | Hemagglutinin | protein | 170 | 51% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, D, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.63 | 0.82 | 26 | empty |
| 2 | 242 | 0.63 | 0.81 | 25 | empty |
| 3 | 231 | 0.62 | 0.81 | 24 | empty |
| 4 | 216 | 0.47 | 0.74 | 29 | NAG, GAL, SIA |
| 5 | 95 | 0.42 | 0.78 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3134 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3130 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 3126 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 88 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4LKG · The structure of hemagglutinin from a avian-origin H7N9 influenza virus… · 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
- Elsewhere: RCSB PDB 4LKG · PDBe 4LKG
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