MolNFT v1 · #139623 · protein
The structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6 influenza virus in complex with avian receptor analog lsta
5XLC: “The structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6 influenza virus in complex with…”. X-ray diffraction, 2 ligands (NAG, SIA), 5 pockets (best druggability 0.57). MolNFT v1 #139623 on GenesisL1: 3D…
- PDB
- 5XLC
- 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
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 319 | 8% helix, 37% 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 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
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 | 239 | 0.57 | 0.79 | 33 | empty |
| 2 | 213 | 0.55 | 0.79 | 29 | empty |
| 3 | 104 | 0.46 | 0.80 | 24 | empty |
| 4 | 62 | 0.36 | 0.78 | 17 | empty |
| 5 | 52 | 0.30 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3028 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 2978 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 230 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5XLC · 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 5XLC · PDBe 5XLC · UniProt A3KF09
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