Research workbench
Influenza hemagglutinin A/BANGKOK/01/1979(H3N2)
Analyse Influenza hemagglutinin A/BANGKOK/01/1979(H3N2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XPO
- Type
- protein
- Length
- 1,475 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q1K9S3
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 491 | 25% helix, 29% strand | Q1K9S3 |
| B | Hemagglutinin | protein | 491 | 24% helix, 30% strand | Q1K9S3 |
| C | Hemagglutinin | protein | 493 | 25% helix, 31% strand | Q1K9S3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 13 copies · chains C, A, B
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.84 | 0.87 | 66 | empty |
| 2 | 421 | 0.75 | 0.84 | 58 | empty |
| 3 | 460 | 0.73 | 0.83 | 61 | empty |
| 4 | 93 | 0.73 | 0.95 | 18 | empty |
| 5 | 459 | 0.72 | 0.82 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2286 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2273 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2273 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 6XPO · Influenza hemagglutinin A/Bangkok/01/1979(H3N2) · 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 Q1K9S3
- Elsewhere: RCSB PDB 6XPO · PDBe 6XPO · UniProt Q1K9S3
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