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Crystal structure of influenza a virus H5 hemagglutinin globular head in complex with the Fab of antibody FLD21.140
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
- 6A67
- Type
- protein
- Length
- 1,277 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FLD21.140 heavy chain; FLD21.140 light chain; Hemagglutinin
- UniProt
- Q6Q794
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, C | FLD21.140 heavy chain | protein | 222 | 7% helix, 53% strand | — |
| L, D | FLD21.140 light chain | protein | 212 | 8% helix, 51% strand | — |
| B | Hemagglutinin | protein | 204 | 11% helix, 39% strand | Q6Q794 |
| A | Hemagglutinin | protein | 205 | 12% helix, 40% strand | Q6Q794 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.82 | 0.84 | 115 | empty |
| 2 | 203 | 0.63 | 0.83 | 31 | empty |
| 3 | 313 | 0.61 | 0.79 | 47 | empty |
| 4 | 363 | 0.54 | 0.73 | 56 | empty |
| 5 | 60 | 0.42 | 0.82 | 18 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1730 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1724 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 690 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 679 Ų buried · 12 hydrogen bonds · protein-protein
- L–C · 386 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6A67 · 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 Q6Q794
- Elsewhere: RCSB PDB 6A67 · PDBe 6A67 · UniProt Q6Q794
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