MolNFT v1 · #97180 · protein
Structure of an airborne transmissible avian influenza H5 hemagglutinin mutant from the influenza virus A/INDONESIA/5/2005 complexed with avian receptor analog lsta
4K66: “Structure of an airborne transmissible avian influenza H5 hemagglutinin mutant from the influenza virus…”. X-ray diffraction, 3 ligands (GAL, SIA, NAG), 17 pockets (best druggability 0.64). MolNFT v1 #97180 on GenesisL1: 3D…
- PDB
- 4K66
- 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
- GAL, SIA, NAG
- Pockets
- 17 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemagglutinin | protein | 321 | 9% helix, 40% strand | A8HWY8 |
| B, D, F, H | Hemagglutinin | protein | 164 | 51% helix, 11% strand | A8HWY8 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
- 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
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.64 | 0.79 | 44 | empty |
| 2 | 324 | 0.62 | 0.79 | 45 | empty |
| 3 | 417 | 0.59 | 0.75 | 42 | empty |
| 4 | 257 | 0.57 | 0.78 | 36 | empty |
| 5 | 249 | 0.56 | 0.78 | 41 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2624 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2609 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2568 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2564 Ų buried · 36 hydrogen bonds · protein-protein
- A–F · 177 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4K66 · Structure of an airborne transmissible avian influenza H5 hemagglutinin mutant from the… · the same entry in another collection · chain B against B, 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 4K66 · PDBe 4K66 · UniProt A8HWY8
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