MolNFT v1 · #155862 · protein
Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin
6LKS · Hemagglutinin HA1 chain: “Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.82). MolNFT v1 #155862 on GenesisL1…
- 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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