Research workbench
Crystal structure of Fab 54-4H03 bound to H1 influenza hemagglutinin
Analyse Crystal structure of Fab 54-4H03 bound to H1 influenza hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WJ1
- Type
- protein
- Length
- 2,820 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Fab 54-4H03 heavy chain; Fab 54-4H03…
- UniProt
- A0A3S7XTA4, A0A3S5H8L7
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 324 | 8% helix, 39% strand | A0A3S7XTA4 |
| C | Hemagglutinin HA1 chain | protein | 324 | 8% helix, 38% strand | A0A3S7XTA4 |
| E | Hemagglutinin HA1 chain | protein | 326 | 7% helix, 39% strand | A0A3S7XTA4 |
| B | Hemagglutinin HA2 chain | protein | 175 | 53% helix, 15% strand | A0A3S5H8L7 |
| D, F | Hemagglutinin HA2 chain | protein | 171 | 53% helix, 16% strand | A0A3S5H8L7 |
| H, J, G | Fab 54-4H03 heavy chain | protein | 228 | 7% helix, 54% strand | — |
| L, K, I | Fab 54-4H03 light chain | protein | 215 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, G, C, E, F, B, I, D, K
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, E
- FUC · alpha-L-fucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.85 | 0.96 | 30 | empty |
| 2 | 754 | 0.81 | 0.84 | 97 | empty |
| 3 | 321 | 0.74 | 0.86 | 43 | empty |
| 4 | 272 | 0.73 | 0.86 | 44 | empty |
| 5 | 272 | 0.72 | 0.86 | 42 | empty |
Interfaces
27 interfaces between chains.
- E–F · 2843 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2838 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2795 Ų buried · 40 hydrogen bonds · protein-protein
- J–K · 2041 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 1999 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 19 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6WJ1 · Crystal structure of Fab 54-4H03 bound to H1 influenza hemagglutinin · 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 A0A3S7XTA4
- Every structure of UniProt A0A3S5H8L7
- Elsewhere: RCSB PDB 6WJ1 · PDBe 6WJ1 · UniProt A0A3S7XTA4 · UniProt A0A3S5H8L7
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