MolNFT v1 · #139620 · protein
The structure of hemagglutinin G228S mutant from an avian-origin H4N6 influenza virus in complex with avian receptor analog lsta
5XL9: “The structure of hemagglutinin G228S mutant from an avian-origin H4N6 influenza virus in complex with avian…”. X-ray diffraction, 2 ligands (NAG, SIA), 20 pockets (best druggability 0.83). MolNFT v1 #139620 on GenesisL1: 3D…
- PDB
- 5XL9
- Type
- protein
- Length
- 1,458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A3KF09
- Ligands
- NAG, SIA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin | protein | 486 | 23% helix, 31% strand | A3KF09 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.83 | 0.90 | 34 | empty |
| 2 | 523 | 0.77 | 0.85 | 72 | empty |
| 3 | 715 | 0.77 | 0.81 | 75 | empty |
| 4 | 844 | 0.76 | 0.80 | 69 | empty |
| 5 | 530 | 0.74 | 0.82 | 66 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2380 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2374 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2283 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5XL9 · The structure of hemagglutinin G228S mutant from an avian-origin H4N6 influenza virus in… · 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 5XL9 · PDBe 5XL9 · UniProt A3KF09
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