MolNFT v1 · #139619 · protein
The structure of hemagglutinin G228S mutant from a avian-origin H4N6 influenza virus (A/DUCK/CZECH/1956)
5XL8: “The structure of hemagglutinin G228S mutant from a avian-origin H4N6 influenza virus (A/DUCK/CZECH/1956)”. X-ray diffraction, 1 ligand (NAG), 18 pockets (best druggability 0.83). MolNFT v1 #139619 on GenesisL1: 3D structure, binding…
- PDB
- 5XL8
- 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
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin | protein | 486 | 24% helix, 30% strand | A3KF09 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.83 | 0.89 | 51 | empty |
| 2 | 578 | 0.75 | 0.82 | 69 | empty |
| 3 | 544 | 0.74 | 0.82 | 67 | empty |
| 4 | 342 | 0.73 | 0.85 | 49 | empty |
| 5 | 565 | 0.73 | 0.81 | 64 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2320 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2292 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2288 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5XL8 · The structure of hemagglutinin G228S mutant from a avian-origin H4N6 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
- Every structure of UniProt A3KF09
- Elsewhere: RCSB PDB 5XL8 · PDBe 5XL8 · UniProt A3KF09
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