Research workbench
Crystal structure of influenza a virus H5 hemagglutinin globular head in complex with the Fab of antibody AVFLUIGG01
Analyse Crystal structure of influenza a virus H5 hemagglutinin globular head in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IUT
- Type
- protein
- Length
- 641 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AVFLUIGG01 heavy chain; AVFLUIGG01 light chain; Hemagglutinin
- UniProt
- Q1WDM0
- Ligands
- NAG, FUC
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | AVFLUIGG01 heavy chain | protein | 219 | 5% helix, 49% strand | — |
| L | AVFLUIGG01 light chain | protein | 214 | 9% helix, 49% strand | — |
| A | Hemagglutinin | protein | 208 | 12% helix, 36% strand | Q1WDM0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains H, A
- FUC · alpha-L-fucopyranose · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.64 | 0.75 | 67 | empty |
| 2 | 155 | 0.45 | 0.76 | 29 | empty |
| 3 | 92 | 0.41 | 0.78 | 20 | empty |
| 4 | 50 | 0.27 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1986 Ų buried · 20 hydrogen bonds · protein-protein
- H–A · 678 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 330 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6IUT · Crystal structure of influenza A virus H5 hemagglutinin globular head in complex with the… · the same entry in another collection · chain H against H, 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 Q1WDM0
- Elsewhere: RCSB PDB 6IUT · PDBe 6IUT · UniProt Q1WDM0
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