Research workbench
Crystal structure of hemagglutinin from taiwan (2013) H6N1 influenza virus in complex with lsta
Analyse Crystal structure of hemagglutinin from taiwan (2013) H6N1 influenza virus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XKF
- 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, GAL, SIA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 329 | 9% helix, 39% strand | — |
| B, D | Hemagglutinin HA2 chain | protein | 173 | 57% helix, 13% strand | — |
| C | Hemagglutinin HA1 chain | protein | 326 | 10% helix, 38% strand | — |
| E | Hemagglutinin HA1 chain | protein | 325 | 9% helix, 37% strand | — |
| F | Hemagglutinin HA2 chain | protein | 172 | 57% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.87 | 0.89 | 117 | empty |
| 2 | 122 | 0.80 | 0.98 | 21 | empty |
| 3 | 887 | 0.74 | 0.78 | 84 | empty |
| 4 | 239 | 0.70 | 0.86 | 31 | empty |
| 5 | 52 | 0.63 | 0.95 | 21 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2748 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2728 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2716 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1341 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1301 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4XKF · Crystal structure of hemagglutinin from Taiwan (2013) H6N1 influenza virus in complex… · 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 4XKF · PDBe 4XKF
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