Research workbench
Crystal structure of the A/HONG KONG/1/1968 (H3N2) influenza virus hemagglutinin E190D mutant apo form
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
- 6BKM
- Type
- protein
- Length
- 1,469 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q91MA7, P03436
- Ligands
- TAM, NAG, BMA, MAN
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 321 | 10% helix, 41% strand | Q91MA7 |
| B | Hemagglutinin | protein | 172 | 51% helix, 15% strand | P03436 |
| C, E | Hemagglutinin | protein | 317 | 10% helix, 42% strand | Q91MA7 |
| D, F | Hemagglutinin | protein | 171 | 51% helix, 15% strand | P03436 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C, B, E, D, F
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, E, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.87 | 0.89 | 41 | empty |
| 2 | 575 | 0.86 | 0.91 | 55 | empty |
| 3 | 307 | 0.77 | 0.89 | 48 | empty |
| 4 | 606 | 0.77 | 0.83 | 75 | empty |
| 5 | 477 | 0.72 | 0.82 | 51 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3029 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2981 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2935 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 1508 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1484 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6BKM · Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D… · 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 6BKM · PDBe 6BKM · UniProt Q91MA7 · UniProt P03436
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