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The crystal structure of hemagglutinin from A/HONG KONG/61/2016 H7N9 influenza virus
Analyse The crystal structure of hemagglutinin from A/HONG KONG/61/2016 H7N9 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D7C
- Type
- protein
- Length
- 2,922 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- A0A0C4ZYE2, S4V1Z7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin HA1 chain | protein | 316 | 9% helix, 41% strand | A0A0C4ZYE2 |
| B, D, F, H, J, L | Hemagglutinin HA2 chain | protein | 171 | 51% helix, 13% strand | S4V1Z7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, E, C, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.85 | 0.98 | 24 | empty |
| 2 | 190 | 0.84 | 0.98 | 23 | empty |
| 3 | 263 | 0.82 | 0.94 | 30 | empty |
| 4 | 163 | 0.81 | 0.97 | 27 | empty |
| 5 | 249 | 0.81 | 0.93 | 30 | empty |
Interfaces
30 interfaces between chains.
- K–L · 3238 Ų buried · 51 hydrogen bonds · protein-protein
- I–J · 3230 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3226 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 3213 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 3212 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6D7C · The crystal structure of hemagglutinin from A/Hong Kong/61/2016 H7N9 influenza virus · 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 A0A0C4ZYE2
- Every structure of UniProt S4V1Z7
- Elsewhere: RCSB PDB 6D7C · PDBe 6D7C · UniProt A0A0C4ZYE2 · UniProt S4V1Z7
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