Research workbench
Crystal structure of a H5N1 influenza virus hemagglutinin.
Analyse Crystal structure of a H5N1 influenza virus hemagglutinin. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FK0
- Type
- protein
- Length
- 4,473 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q | Hemagglutinin | protein | 322 | 7% helix, 39% strand | — |
| B, D, F, H, J, L, N, P, R | Hemagglutinin | protein | 175 | 56% helix, 9% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, C, E, I, Q, G, K, M, O
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains Q
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 | 191 | 0.84 | 0.98 | 23 | empty |
| 2 | 188 | 0.83 | 0.97 | 24 | empty |
| 3 | 274 | 0.83 | 0.94 | 30 | empty |
| 4 | 982 | 0.83 | 0.84 | 52 | empty |
| 5 | 261 | 0.82 | 0.94 | 29 | empty |
Interfaces
37 interfaces between chains.
- E–F · 2816 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 2812 Ų buried · 38 hydrogen bonds · protein-protein
- K–L · 2788 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2736 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 2724 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 2FK0 · Crystal Structure of a H5N1 influenza virus hemagglutinin. · 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
- Elsewhere: RCSB PDB 2FK0 · PDBe 2FK0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.