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The crystal structure of hemagglutinin from A/TAIWAN/1/2013 in complex with 6'SLN
Analyse The crystal structure of hemagglutinin from A/TAIWAN/1/2013 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WSV
- Type
- protein
- Length
- 1,479 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- Ligands
- NAG, SIA
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 325 | 10% helix, 36% strand | — |
| B, D, F | Hemagglutinin HA2 chain | protein | 168 | 54% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.82 | 0.94 | 42 | empty |
| 2 | 763 | 0.81 | 0.85 | 91 | empty |
| 3 | 127 | 0.81 | 0.98 | 18 | empty |
| 4 | 1147 | 0.75 | 0.77 | 116 | empty |
| 5 | 210 | 0.70 | 0.87 | 33 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2765 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2755 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2755 Ų buried · 38 hydrogen bonds · protein-protein
- D–F · 1323 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1269 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4WSV · The crystal structure of hemagglutinin from A/Taiwan/1/2013 in complex with 6'SLN · 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 4WSV · PDBe 4WSV
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