MolNFT v1 · #107818 · protein
Structure of the A_EQUINE_NEWMARKET_2_93 H3 haemagglutinin in complex with 6SO4-3SLN
4UNY · Hay subunit of haemagglutinin: “Structure of the A_EQUINE_NEWMARKET_2_93 H3 haemagglutinin in complex with 6SO4-3SLN”. X-ray diffraction, 7 ligands (NGS, NAG, BMA), 18 pockets (best druggability 0.85). MolNFT v1 #107818 on…
- PDB
- 4UNY
- Type
- protein
- Length
- 1,485 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hay subunit of haemagglutinin; H3 haemagglutinin HA2 chain
- UniProt
- Q82847
- Ligands
- NGS, NAG, BMA, MAN, GAL, SIA, FUC
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hay subunit of haemagglutinin | protein | 317 | 10% helix, 39% strand | Q82847 |
| B | H3 haemagglutinin HA2 chain | protein | 173 | 57% helix, 15% strand | — |
| C | Hay subunit of haemagglutinin | protein | 330 | 9% helix, 38% strand | Q82847 |
| D, F | H3 haemagglutinin HA2 chain | protein | 172 | 52% helix, 16% strand | — |
| E | Hay subunit of haemagglutinin | protein | 321 | 10% helix, 37% strand | Q82847 |
Ligands and binding sites
- NGS · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose · ligand · 3 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, C, B, E, D, F
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains C, E, A
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.85 | 0.92 | 35 | empty |
| 2 | 267 | 0.85 | 0.95 | 32 | empty |
| 3 | 1192 | 0.77 | 0.79 | 142 | empty |
| 4 | 620 | 0.71 | 0.79 | 60 | empty |
| 5 | 494 | 0.71 | 0.81 | 59 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3308 Ų buried · 55 hydrogen bonds · protein-protein
- E–F · 3171 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3066 Ų buried · 46 hydrogen bonds · protein-protein
- B–F · 1535 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1516 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 4UNY · Structure of the A_Equine_Newmarket_2_93 H3 haemagglutinin in complex with 6SO4-3SLN · 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 4UNY · PDBe 4UNY · UniProt Q82847
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