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Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin
Analyse Effects of zinc ion on oligomerization and pH stability of influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKS
- Type
- protein
- Length
- 2,914 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- A7LI25
- Ligands
- NAG, MAN, BMA, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, A, C, E | Hemagglutinin HA1 chain | protein | 321 | 10% helix, 35% strand | A7LI25 |
| L, B, D, F, H, J | Hemagglutinin HA2 chain | protein | 165 | 39% helix, 14% strand | A7LI25 |
| G, I | Hemagglutinin HA1 chain | protein | 320 | 11% helix, 38% strand | A7LI25 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains K, A, C, E, G, I
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, K, C, E, G
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, K
- ZN · Zinc ion · metal · 3 copies · chains K, A, G, I
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 | 957 | 0.82 | 0.84 | 104 | empty |
| 2 | 928 | 0.81 | 0.83 | 96 | empty |
| 3 | 175 | 0.81 | 0.96 | 18 | empty |
| 4 | 125 | 0.79 | 0.97 | 18 | empty |
| 5 | 1021 | 0.79 | 0.80 | 101 | empty |
Interfaces
31 interfaces between chains.
- E–F · 2649 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 2637 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2633 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2632 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 2618 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 6LKS · Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin · the same entry in another collection · chain K against K, 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 A7LI25
- Elsewhere: RCSB PDB 6LKS · PDBe 6LKS · UniProt A7LI25
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