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Crystal structure of the A/HONG KONG/1/1968 (H3N2) influenza virus hemagglutinin in complex with small molecule N-cyclohexyltaurine
Analyse Crystal structure of the A/HONG KONG/1/1968 (H3N2) influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CEX
- Type
- protein
- Length
- 1,465 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q91MA7, P03436
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 317 | 10% helix, 42% strand | Q91MA7 |
| B, D | Hemagglutinin | protein | 171 | 54% helix, 15% strand | P03436 |
| C | Hemagglutinin | protein | 316 | 10% helix, 42% strand | Q91MA7 |
| E | Hemagglutinin | protein | 318 | 10% helix, 42% strand | Q91MA7 |
| F | Hemagglutinin | protein | 172 | 53% helix, 15% strand | P03436 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, C, B, E, D, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, E, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, E, D, F
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.87 | 0.89 | 41 | empty |
| 2 | 253 | 0.85 | 0.96 | 30 | empty |
| 3 | 732 | 0.75 | 0.80 | 69 | empty |
| 4 | 543 | 0.73 | 0.81 | 53 | empty |
| 5 | 242 | 0.71 | 0.87 | 23 | NHE |
Interfaces
15 interfaces between chains.
- A–B · 2939 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2919 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2907 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 1492 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1492 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 6CEX · Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in… · 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
- Every structure of UniProt P03436
- Elsewhere: RCSB PDB 6CEX · PDBe 6CEX · UniProt Q91MA7 · UniProt P03436
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