Research workbench
Structure of an avian influenza H5 hemagglutinin from the influenza virus A/INDONESIA/5/2005
Analyse Structure of an avian influenza H5 hemagglutinin from the influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K62
- Type
- protein
- Length
- 1,940 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A8HWY8
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemagglutinin | protein | 321 | 9% helix, 41% strand | A8HWY8 |
| B, D, F, H | Hemagglutinin | protein | 164 | 52% helix, 13% strand | A8HWY8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.63 | 0.80 | 44 | empty |
| 2 | 308 | 0.60 | 0.78 | 49 | empty |
| 3 | 342 | 0.57 | 0.76 | 42 | empty |
| 4 | 176 | 0.56 | 0.80 | 31 | empty |
| 5 | 232 | 0.54 | 0.77 | 41 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2689 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2650 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2558 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2555 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4K62 · Structure of an avian influenza H5 hemagglutinin from the influenza virus… · 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 A8HWY8
- Elsewhere: RCSB PDB 4K62 · PDBe 4K62 · UniProt A8HWY8
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