MolNFT v1 · #139612 · protein
The structure of hemagglutinin from an avian-origin H4N6 influenza virus
5XL1: “The structure of hemagglutinin from an avian-origin H4N6 influenza virus”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.58). MolNFT v1 #139612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XL1
- 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
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | 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 · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.58 | 0.80 | 36 | empty |
| 2 | 243 | 0.56 | 0.78 | 31 | empty |
| 3 | 108 | 0.47 | 0.80 | 23 | empty |
| 4 | 135 | 0.44 | 0.76 | 25 | empty |
| 5 | 128 | 0.41 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2983 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 2953 Ų buried · 46 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
- 5XL1 · The structure of hemagglutinin from an avian-origin H4N6 influenza virus · the same entry in another collection · chain B against B, 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 5XL1 · PDBe 5XL1 · UniProt A3KF09
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