Research workbench
Structure of influenza H2 hemagglutinin with human receptor
Analyse Structure of influenza H2 hemagglutinin with human receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WR1
- Type
- protein
- Length
- 1,465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, BMA, GAL, SIA, MAN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 490 | 23% helix, 32% strand | — |
| B | Hemagglutinin | protein | 490 | 23% helix, 31% strand | — |
| C | Hemagglutinin | protein | 485 | 24% helix, 31% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains B, C, A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains B, C
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.81 | 0.83 | 103 | empty |
| 2 | 151 | 0.81 | 0.97 | 25 | empty |
| 3 | 442 | 0.80 | 0.88 | 83 | empty |
| 4 | 353 | 0.73 | 0.84 | 47 | empty |
| 5 | 232 | 0.71 | 0.86 | 40 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2525 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2455 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2386 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 glycan (disulfide, glycosylation).
Compared structures
- 2WR1 · structure of influenza H2 hemagglutinin with human receptor · 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 2WR1 · PDBe 2WR1
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