MolNFT v1 · #114387 · protein
Crystal structure of hemagglutinin of A/CHICKEN/GUANGDONG/S1311/2010 (H6N6)
5BNY: “Crystal structure of hemagglutinin of A/CHICKEN/GUANGDONG/S1311/2010 (H6N6)”. X-ray diffraction, 1 ligand (NAG), 17 pockets (best druggability 0.86). MolNFT v1 #114387 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BNY
- Type
- protein
- Length
- 1,492 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A0A067YZV9
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 324 | 9% helix, 41% strand | A0A067YZV9 |
| B | Hemagglutinin | protein | 171 | 56% helix, 13% strand | A0A067YZV9 |
| D | Hemagglutinin | protein | 173 | 57% helix, 13% strand | A0A067YZV9 |
| F | Hemagglutinin | protein | 176 | 57% helix, 13% strand | A0A067YZV9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.86 | 0.97 | 42 | empty |
| 2 | 935 | 0.83 | 0.84 | 110 | empty |
| 3 | 534 | 0.65 | 0.77 | 48 | empty |
| 4 | 145 | 0.64 | 0.87 | 25 | empty |
| 5 | 208 | 0.63 | 0.83 | 34 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2686 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2644 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2642 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 1464 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1402 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 5BNY · Crystal structure of hemagglutinin of A/Chicken/Guangdong/S1311/2010 (H6N6) · 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 A0A067YZV9
- Elsewhere: RCSB PDB 5BNY · PDBe 5BNY · UniProt A0A067YZV9
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