Research workbench
Structure of the A_EQUINE_NEWMARKET_2_93 H3 haemagglutinin in complex with 3SLN
Analyse Structure of the A_EQUINE_NEWMARKET_2_93 H3 haemagglutinin in complex with 3SLN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UNX
- Type
- protein
- Length
- 1,473 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, SIA, FUC, GAL
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | H3 haemagglutinin HA1 chain | protein | 319 | 8% helix, 40% strand | Q82847 |
| B, D, F | H3 haemagglutinin HA2 chain | protein | 172 | 52% helix, 14% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, D, F
- GAL · beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.86 | 0.88 | 96 | empty |
| 2 | 264 | 0.85 | 0.96 | 30 | empty |
| 3 | 213 | 0.77 | 0.92 | 25 | empty |
| 4 | 226 | 0.76 | 0.90 | 29 | empty |
| 5 | 916 | 0.75 | 0.79 | 70 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3188 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 3161 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3074 Ų buried · 40 hydrogen bonds · protein-protein
- D–F · 1567 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1540 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4UNX · Structure of the A_Equine_Newmarket_2_93 H3 haemagglutinin in complex with 3SLN · 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 4UNX · PDBe 4UNX · UniProt Q82847
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