MolNFT v1 · #114487 · protein
Crystal structure of hemagglutinin of A/CHICKEN/GUANGDONG/S1311/2010 (H6N6) in complex with avian-like receptor lsta
5BQY · Hemagglutinin HA1 chain: “Crystal structure of hemagglutinin of A/CHICKEN/GUANGDONG/S1311/2010 (H6N6) in complex with avian-like…”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 13 pockets (best druggability 0.88). MolNFT v1 #114487…
- PDB
- 5BQY
- Type
- protein
- Length
- 1,490 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- A0A067Z050, A0A067YZ73
- Ligands
- NAG, GAL, SIA
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 324 | 10% helix, 42% strand | A0A067Z050 |
| B | Hemagglutinin HA2 chain | protein | 171 | 55% helix, 13% strand | A0A067YZ73 |
| D | Hemagglutinin HA2 chain | protein | 173 | 54% helix, 13% strand | A0A067YZ73 |
| F | Hemagglutinin HA2 chain | protein | 174 | 54% helix, 13% strand | A0A067YZ73 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, E, F, C
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.88 | 0.90 | 142 | empty |
| 2 | 979 | 0.74 | 0.77 | 90 | empty |
| 3 | 337 | 0.65 | 0.80 | 48 | empty |
| 4 | 218 | 0.63 | 0.83 | 39 | empty |
| 5 | 446 | 0.63 | 0.77 | 48 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2674 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2644 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2625 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 1373 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1363 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 13 glycan (disulfide, N-glycosylation).
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 A0A067Z050
- Every structure of UniProt A0A067YZ73
- Elsewhere: RCSB PDB 5BQY · PDBe 5BQY · UniProt A0A067Z050 · UniProt A0A067YZ73
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