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Crystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10N8 influenza virus in complex with 3'-SLN
Analyse Crystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10N8 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XQU
- Type
- protein
- Length
- 1,453 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.25
- Source
- Influenza A virus
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- A0A059T4A1
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 3.25 · 6 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 318 | 8% helix, 39% strand | A0A059T4A1 |
| B | Hemagglutinin HA2 | protein | 169 | 55% helix, 12% strand | A0A059T4A1 |
| C | Hemagglutinin HA1 | protein | 318 | 9% helix, 40% strand | A0A059T4A1 |
| D | Hemagglutinin HA2 | protein | 165 | 58% helix, 7% strand | A0A059T4A1 |
| E | Hemagglutinin HA1 | protein | 317 | 8% helix, 36% strand | A0A059T4A1 |
| F | Hemagglutinin HA2 | protein | 166 | 46% helix, 7% strand | A0A059T4A1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, E, C, B
- 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
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.87 | 0.89 | 95 | empty |
| 2 | 415 | 0.84 | 0.92 | 40 | empty |
| 3 | 187 | 0.80 | 0.95 | 31 | empty |
| 4 | 140 | 0.78 | 0.96 | 28 | empty |
| 5 | 307 | 0.74 | 0.86 | 39 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3217 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 3155 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3126 Ų buried · 40 hydrogen bonds · protein-protein
- D–F · 1631 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1507 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4XQU · Crystal structure of hemagglutinin from jiangxi-donghu (2013) H10N8 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 A0A059T4A1
- Elsewhere: RCSB PDB 4XQU · PDBe 4XQU · UniProt A0A059T4A1
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