MolNFT v1 · #88565 · protein
Structure of the A_MALLARD_SWEDEN_51_2002 H10 avian haemmaglutinin
4CYV · Hemagglutinin: “Structure of the A_MALLARD_SWEDEN_51_2002 H10 avian haemmaglutinin”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #88565 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4CYV
- Type
- protein
- Length
- 1,472 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- E0YNJ7
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 318 | 9% helix, 40% strand | E0YNJ7 |
| B, D, F | Hemagglutinin | protein | 172 | 57% helix, 13% strand | E0YNJ7 |
| C, E | Hemagglutinin | protein | 319 | 9% helix, 40% strand | E0YNJ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 4 copies
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, F, C, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.83 | 0.84 | 132 | empty |
| 2 | 442 | 0.83 | 0.90 | 40 | empty |
| 3 | 98 | 0.76 | 0.97 | 18 | EDO |
| 4 | 300 | 0.76 | 0.88 | 47 | empty |
| 5 | 87 | 0.75 | 0.97 | 17 | EDO |
Interfaces
15 interfaces between chains.
- A–B · 3227 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3224 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 3179 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 1518 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1480 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 4CYV · Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin · 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 4CYV · PDBe 4CYV · UniProt E0YNJ7
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