Research workbench
Crystal structure of H1N1PDM hemagglutinin
Analyse Crystal structure of H1N1PDM hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M6S
- Type
- protein
- Length
- 2,958 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C5MV42
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 325 | 9% helix, 39% strand | C5MV42 |
| B | Hemagglutinin | protein | 169 | 56% helix, 15% strand | C5MV42 |
| C, E | Hemagglutinin | protein | 323 | 9% helix, 40% strand | C5MV42 |
| D, F, L | Hemagglutinin | protein | 171 | 56% helix, 15% strand | C5MV42 |
| G | Hemagglutinin | protein | 322 | 9% helix, 40% strand | C5MV42 |
| H, J | Hemagglutinin | protein | 170 | 55% helix, 15% strand | C5MV42 |
| I | Hemagglutinin | protein | 322 | 9% helix, 40% strand | C5MV42 |
| K | Hemagglutinin | protein | 321 | 9% helix, 39% strand | C5MV42 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains C, G, I, K, A, E
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.86 | 0.87 | 140 | empty |
| 2 | 251 | 0.83 | 0.95 | 30 | empty |
| 3 | 168 | 0.75 | 0.92 | 26 | empty |
| 4 | 1023 | 0.75 | 0.78 | 113 | empty |
| 5 | 280 | 0.75 | 0.88 | 47 | empty |
Interfaces
26 interfaces between chains.
- A–B · 2796 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2779 Ų buried · 41 hydrogen bonds · protein-protein
- I–J · 2770 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2759 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2735 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 10 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 3M6S · Crystal structure of H1N1pdm Hemagglutinin · 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 C5MV42
- Elsewhere: RCSB PDB 3M6S · PDBe 3M6S · UniProt C5MV42
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