Research workbench
Structure of influenza H2 duck ontario hemagglutinin with human receptor
Analyse Structure of influenza H2 duck ontario 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
- 2WR4
- Type
- protein
- Length
- 1,457 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 485 | 22% helix, 29% strand | — |
| B, C | Hemagglutinin | protein | 486 | 23% helix, 30% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.82 | 0.98 | 22 | empty |
| 2 | 1030 | 0.80 | 0.82 | 101 | empty |
| 3 | 356 | 0.76 | 0.87 | 49 | empty |
| 4 | 100 | 0.76 | 0.96 | 24 | empty |
| 5 | 939 | 0.76 | 0.79 | 99 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2417 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2377 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2321 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 2WR4 · structure of influenza H2 duck Ontario 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 2WR4 · PDBe 2WR4
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