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Structure of the A_EQUINE_NEWMARKET_2_93 H3 haemagglutinin
Analyse Structure of the A_EQUINE_NEWMARKET_2_93 H3 haemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UNW
- Type
- protein
- Length
- 1,478 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H3 haemagglutinin HA1 chain; H3 haemagglutinin HA2 chain
- UniProt
- Q82847
- Ligands
- NAG, MAN, BMA, FUL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H3 haemagglutinin HA1 chain | protein | 320 | 10% helix, 39% strand | Q82847 |
| B, D, F | H3 haemagglutinin HA2 chain | protein | 172 | 54% helix, 16% strand | — |
| C, E | H3 haemagglutinin HA1 chain | protein | 321 | 10% helix, 41% strand | Q82847 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, E, B, C, D, F
- MAN · alpha-D-mannopyranose · sugar · 11 copies
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains E, A, C
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.86 | 0.87 | 125 | empty |
| 2 | 293 | 0.85 | 0.95 | 34 | empty |
| 3 | 89 | 0.74 | 0.96 | 22 | empty |
| 4 | 98 | 0.73 | 0.95 | 23 | empty |
| 5 | 86 | 0.72 | 0.96 | 21 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3160 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3160 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3076 Ų buried · 46 hydrogen bonds · protein-protein
- B–F · 1475 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1452 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 4UNW · Structure of the A_Equine_Newmarket_2_93 H3 haemagglutinin · 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 Q82847
- Elsewhere: RCSB PDB 4UNW · PDBe 4UNW · UniProt Q82847
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