MolNFT v1 · #114488 · protein
Crystal structure of hemagglutinin of A/CHICKEN/GUANGDONG/S1311/2010 (H6N6) in complex with human-like receptor lstc
5BQZ · Hemagglutinin HA1 chain: “Crystal structure of hemagglutinin of A/CHICKEN/GUANGDONG/S1311/2010 (H6N6) in complex with human-like…”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 14 pockets (best druggability 0.86). MolNFT v1 #114488…
- PDB
- 5BQZ
- Type
- protein
- Length
- 1,481 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin
- UniProt
- A0A067YZV9
- Ligands
- NAG, GAL, SIA
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 323 | 10% helix, 39% strand | A0A067YZV9 |
| B | Hemagglutinin | protein | 170 | 55% helix, 12% strand | A0A067YZV9 |
| D | Hemagglutinin | protein | 173 | 56% helix, 13% strand | A0A067YZV9 |
| F | Hemagglutinin | protein | 169 | 56% helix, 14% strand | A0A067YZV9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, F, A, C, E
- GAL · beta-D-galactopyranose · sugar · 3 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.86 | 0.97 | 37 | empty |
| 2 | 948 | 0.85 | 0.86 | 138 | empty |
| 3 | 853 | 0.73 | 0.78 | 79 | empty |
| 4 | 366 | 0.65 | 0.80 | 51 | empty |
| 5 | 354 | 0.65 | 0.79 | 50 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2594 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2572 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2556 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1363 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 1330 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5BQZ · Crystal structure of hemagglutinin of A/Chicken/Guangdong/S1311/2010 (H6N6) in complex… · the same entry in another collection · chain C against C, 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 5BQZ · PDBe 5BQZ · UniProt A0A067YZV9
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