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Influenza hemagglutinin H3 A/HONG KONG/1/1968 in complex with designed inhibitor protein HSB.2A
Analyse Influenza hemagglutinin H3 A/HONG KONG/1/1968 in complex with designed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KUY
- Type
- protein
- Length
- 1,693 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; Designed influenza inhibitor HSB.2A
- UniProt
- Q91MA7
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 9 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 319 | 10% helix, 39% strand | Q91MA7 |
| B | Hemagglutinin HA2 | protein | 176 | 55% helix, 13% strand | Q91MA7 |
| C | Hemagglutinin HA1 | protein | 316 | 10% helix, 43% strand | Q91MA7 |
| D | Hemagglutinin HA2 | protein | 172 | 54% helix, 15% strand | Q91MA7 |
| E | Hemagglutinin HA1 | protein | 317 | 10% helix, 42% strand | Q91MA7 |
| F | Hemagglutinin HA2 | protein | 171 | 57% helix, 13% strand | Q91MA7 |
| G | Designed influenza inhibitor HSB.2A | protein | 84 | 25% helix, 48% strand | — |
| H | Designed influenza inhibitor HSB.2A | protein | 85 | 25% helix, 49% strand | — |
| I | Designed influenza inhibitor HSB.2A | protein | 53 | 28% helix, 19% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C, E, D, F, B
- BMA · beta-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.87 | 0.88 | 52 | empty |
| 2 | 248 | 0.84 | 0.95 | 26 | empty |
| 3 | 618 | 0.77 | 0.83 | 79 | empty |
| 4 | 262 | 0.72 | 0.86 | 31 | empty |
| 5 | 612 | 0.71 | 0.79 | 64 | empty |
Interfaces
18 interfaces between chains.
- A–B · 3038 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2962 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2890 Ų buried · 41 hydrogen bonds · protein-protein
- B–F · 1582 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1468 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5KUY · Influenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with designed inhibitor protein… · 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 Q91MA7
- Elsewhere: RCSB PDB 5KUY · PDBe 5KUY · UniProt Q91MA7
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