Research workbench
Crystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918 influenza virus hemagglutinin.
Analyse Crystal structure of the designed inhibitor protein F-HB80.4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EEF
- Type
- protein
- Length
- 1,627 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; F-HB80.4, designed hemagglutinin…
- UniProt
- Q9WFX3
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 325 | 10% helix, 40% strand | Q9WFX3 |
| B, D | Hemagglutinin HA2 chain | protein | 173 | 53% helix, 13% strand | Q9WFX3 |
| C, E | Hemagglutinin HA1 chain | protein | 323 | 9% helix, 41% strand | Q9WFX3 |
| F | Hemagglutinin HA2 chain | protein | 171 | 48% helix, 11% strand | Q9WFX3 |
| G | F-HB80.4, designed hemagglutinin binding protein | protein | 45 | 42% helix, 0% strand | — |
| H, I | F-HB80.4, designed hemagglutinin binding protein | protein | 47 | 51% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.84 | 0.85 | 105 | empty |
| 2 | 298 | 0.82 | 0.93 | 48 | empty |
| 3 | 916 | 0.74 | 0.78 | 98 | empty |
| 4 | 611 | 0.73 | 0.80 | 49 | empty |
| 5 | 511 | 0.73 | 0.82 | 41 | empty |
Interfaces
21 interfaces between chains.
- C–D · 2782 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2778 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2711 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 1409 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1345 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4EEF · Crystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918… · 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 Q9WFX3
- Elsewhere: RCSB PDB 4EEF · PDBe 4EEF · UniProt Q9WFX3
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