Research workbench
Antibody hemagglutinin complexes
Analyse Antibody hemagglutinin complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XRC
- Type
- protein
- Length
- 1,265 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H5.3 Fab light chain; H5.3 Fab heavy chain; Hemagglutinin
- UniProt
- Q6Q9G9
- Ligands
- NAG, FUC
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | H5.3 Fab light chain | protein | 208 | 7% helix, 52% strand | — |
| B | H5.3 Fab heavy chain | protein | 215 | 1% helix, 53% strand | — |
| D | Hemagglutinin | protein | 211 | 11% helix, 42% strand | Q6Q9G9 |
| H | H5.3 Fab heavy chain | protein | 217 | 4% helix, 55% strand | — |
| C | Hemagglutinin | protein | 206 | 12% helix, 42% strand | Q6Q9G9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.72 | 0.77 | 101 | empty |
| 2 | 694 | 0.68 | 0.76 | 62 | empty |
| 3 | 681 | 0.66 | 0.75 | 59 | empty |
| 4 | 50 | 0.65 | 0.96 | 17 | empty |
| 5 | 116 | 0.46 | 0.79 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1951 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1804 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 792 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 568 Ų buried · 6 hydrogen bonds · protein-protein
- H–C · 542 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XRC · Antibody hemagglutinin Complexes · 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 Q6Q9G9
- Elsewhere: RCSB PDB 4XRC · PDBe 4XRC · UniProt Q6Q9G9
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