MolNFT v1 · #88566 · protein
Structure of the A_MALLARD_SWEDEN_51_2002 H10 avian haemmaglutinin in complex with human receptor analog 6-sln
4CYW · Hemagglutinin: “Structure of the A_MALLARD_SWEDEN_51_2002 H10 avian haemmaglutinin in complex with human receptor analog 6-sln”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.84). MolNFT v1 #88566 on…
- PDB
- 4CYW
- Type
- protein
- Length
- 1,474 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- E0YNJ7
- Ligands
- NAG, BMA, MAN, GAL, SIA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 318 | 9% helix, 41% strand | E0YNJ7 |
| B | Hemagglutinin | protein | 172 | 53% helix, 14% strand | E0YNJ7 |
| C, E | Hemagglutinin | protein | 319 | 9% helix, 41% strand | E0YNJ7 |
| D, F | Hemagglutinin | protein | 173 | 52% helix, 13% strand | E0YNJ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, C, D, A, E, F
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains E
- MAN · alpha-D-mannopyranose · sugar · 4 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.84 | 0.85 | 138 | empty |
| 2 | 199 | 0.84 | 0.98 | 25 | empty |
| 3 | 90 | 0.75 | 0.97 | 20 | empty |
| 4 | 337 | 0.74 | 0.86 | 52 | empty |
| 5 | 90 | 0.74 | 0.96 | 20 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3231 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 3202 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3147 Ų buried · 42 hydrogen bonds · protein-protein
- B–F · 1540 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1501 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4CYW · Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with human… · 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 E0YNJ7
- Elsewhere: RCSB PDB 4CYW · PDBe 4CYW · UniProt E0YNJ7
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