Research workbench
Crystal structure of a swine H1N2 influenza virus hemagglutinin
Analyse Crystal structure of a swine H1N2 influenza virus hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F3Z
- Type
- protein
- Length
- 1,456 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q8QT89
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 320 | 8% helix, 38% strand | Q8QT89 |
| B | Hemagglutinin | protein | 171 | 56% helix, 13% strand | Q8QT89 |
| C | Hemagglutinin | protein | 301 | 8% helix, 39% strand | Q8QT89 |
| D | Hemagglutinin | protein | 174 | 55% helix, 11% strand | Q8QT89 |
| E | Hemagglutinin | protein | 320 | 8% helix, 39% strand | Q8QT89 |
| F | Hemagglutinin | protein | 170 | 55% helix, 15% strand | Q8QT89 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.82 | 0.85 | 104 | empty |
| 2 | 102 | 0.77 | 0.97 | 18 | empty |
| 3 | 531 | 0.76 | 0.84 | 51 | empty |
| 4 | 558 | 0.76 | 0.83 | 55 | empty |
| 5 | 179 | 0.76 | 0.92 | 39 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2718 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2652 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2605 Ų buried · 40 hydrogen bonds · protein-protein
- D–F · 1397 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1318 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4F3Z · Crystal structure of a swine H1N2 influenza virus hemagglutinin · the same entry in another collection · chain C against C, 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 Q8QT89
- Elsewhere: RCSB PDB 4F3Z · PDBe 4F3Z · UniProt Q8QT89
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