MolNFT v1 · #157422 · protein
Crystal structure of hemagglutinin from influenza virus A/PHILLIPINES/2/1982 (H3N2)
6MYM: “Crystal structure of hemagglutinin from influenza virus A/PHILLIPINES/2/1982 (H3N2)”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #157422 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MYM
- Type
- protein
- Length
- 1,459 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- D8KS88
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 486 | 26% helix, 31% strand | D8KS88 |
| C | Hemagglutinin | protein | 487 | 26% helix, 30% strand | D8KS88 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.84 | 0.88 | 55 | empty |
| 2 | 1146 | 0.74 | 0.77 | 116 | empty |
| 3 | 255 | 0.73 | 0.87 | 33 | empty |
| 4 | 660 | 0.72 | 0.79 | 62 | empty |
| 5 | 627 | 0.71 | 0.79 | 65 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2420 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2353 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2288 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MYM · Crystal structure of hemagglutinin from influenza virus A/Phillipines/2/1982 (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 D8KS88
- Elsewhere: RCSB PDB 6MYM · PDBe 6MYM · UniProt D8KS88
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