Research workbench
Crystal structure of a H2N2 influenza virus hemagglutinin, human like
Analyse Crystal structure of a H2N2 influenza virus hemagglutinin, human like in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KU5
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- C7S226
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 322 | 10% helix, 41% strand | C7S226 |
| B | Hemagglutinin HA2 chain | protein | 172 | 56% helix, 12% strand | C7S226 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.62 | 0.79 | 44 | empty |
| 2 | 58 | 0.40 | 0.80 | 10 | empty |
| 3 | 112 | 0.37 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2527 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3KU5 · Crystal structure of a H2N2 influenza virus hemagglutinin, human like · 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 C7S226
- Elsewhere: RCSB PDB 3KU5 · PDBe 3KU5 · UniProt C7S226
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