MolNFT v1 · #159965 · protein
Crystal structure of hemagglutinin from influenza virus A/SICHUAN/2/1987 (H3N2)
6P6P: “Crystal structure of hemagglutinin from influenza virus A/SICHUAN/2/1987 (H3N2)”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.81). MolNFT v1 #159965 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6P6P
- Type
- protein
- Length
- 2,931 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- H9XCU1
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 487 | 25% helix, 30% strand | H9XCU1 |
| B | Hemagglutinin | protein | 488 | 25% helix, 31% strand | H9XCU1 |
| C, D, E, F | Hemagglutinin | protein | 489 | 25% helix, 30% strand | H9XCU1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, C, B, E, D, F
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains C, E, D, A, F, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.81 | 0.85 | 79 | empty |
| 2 | 979 | 0.81 | 0.82 | 107 | empty |
| 3 | 243 | 0.77 | 0.90 | 32 | empty |
| 4 | 774 | 0.76 | 0.80 | 80 | empty |
| 5 | 226 | 0.76 | 0.90 | 28 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2383 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 2340 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2327 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2315 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 2276 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 6P6P · Crystal structure of hemagglutinin from influenza virus A/Sichuan/2/1987 (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 H9XCU1
- Elsewhere: RCSB PDB 6P6P · PDBe 6P6P · UniProt H9XCU1
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