MolNFT v1 · #178905 · protein
Crystal structure of the trimeric full length mature hemagglutinin from influenza a virus A/FORT MONMOUTH/1/1947
7JPD · Hemagglutinin HA1 chain: “Crystal structure of the trimeric full length mature hemagglutinin from influenza a virus A/FORT…”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #178905 on…
- PDB
- 7JPD
- Type
- protein
- Length
- 2,895 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q20MG8
- Ligands
- NAG, MAN, BMA, IOD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Hemagglutinin HA1 chain | protein | 323 | 8% helix, 42% strand | Q20MG8 |
| a, b, c, d, e, f | Hemagglutinin HA2 chain | protein | 160 | 53% helix, 14% strand | Q20MG8 |
| F | Hemagglutinin HA1 chain | protein | 320 | 8% helix, 42% strand | Q20MG8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 5 copies
- IOD · Iodide ion · ion · 76 copies · chains A, a, B, b, C, c, F, f, D, d, E, e
- EDO · 1,2-ethanediol · additive · 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 | 263 | 0.85 | 0.96 | 30 | empty |
| 2 | 257 | 0.84 | 0.96 | 30 | empty |
| 3 | 867 | 0.80 | 0.83 | 97 | IOD |
| 4 | 272 | 0.77 | 0.89 | 60 | IOD |
| 5 | 138 | 0.76 | 0.94 | 25 | empty |
Interfaces
31 interfaces between chains.
- D–d · 2764 Ų buried · 41 hydrogen bonds · protein-protein
- A–a · 2741 Ų buried · 45 hydrogen bonds · protein-protein
- C–c · 2741 Ų buried · 41 hydrogen bonds · protein-protein
- F–f · 2723 Ų buried · 41 hydrogen bonds · protein-protein
- E–e · 2711 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 7JPD · Crystal structure of the trimeric full length mature hemagglutinin from influenza A virus… · 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 Q20MG8
- Elsewhere: RCSB PDB 7JPD · PDBe 7JPD · UniProt Q20MG8
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