MolNFT v1 · #110034 · protein
Crystal structure of hemagglutinin from taiwan (2013) H6N1 influenza virus
4XKD · Hemagglutinin HA1 chain: “Crystal structure of hemagglutinin from taiwan (2013) H6N1 influenza virus”. X-ray diffraction, 1 ligand (NAG), 19 pockets (best druggability 0.87). MolNFT v1 #110034 on GenesisL1: 3D structure, binding…
- PDB
- 4XKD
- Type
- protein
- Length
- 1,498 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 330 | 10% helix, 38% strand | — |
| B, F | Hemagglutinin HA2 chain | protein | 172 | 57% helix, 12% strand | — |
| C | Hemagglutinin HA1 chain | protein | 326 | 9% helix, 39% strand | — |
| D | Hemagglutinin HA2 chain | protein | 173 | 54% helix, 13% strand | — |
| E | Hemagglutinin HA1 chain | protein | 325 | 9% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.87 | 0.88 | 139 | empty |
| 2 | 117 | 0.80 | 0.98 | 17 | empty |
| 3 | 373 | 0.65 | 0.79 | 50 | empty |
| 4 | 354 | 0.58 | 0.76 | 49 | empty |
| 5 | 187 | 0.57 | 0.80 | 32 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2755 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2712 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2705 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 1311 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1282 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4XKD · Crystal structure of hemagglutinin from Taiwan (2013) H6N1 influenza 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
- Elsewhere: RCSB PDB 4XKD · PDBe 4XKD
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