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Crystal structure of H6 hemagglutinin G225D mutant from taiwan (2013) H6N1 influenza virus in complex with 3'-sln
Analyse Crystal structure of H6 hemagglutinin G225D mutant from taiwan (2013) H6N1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T0D
- Type
- protein
- Length
- 1,498 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Hemagglutinin HA2 chain
- UniProt
- A0A0J9X268, A0A0J9X267
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 330 | 9% helix, 35% strand | A0A0J9X268 |
| B, D | Hemagglutinin HA2 chain | protein | 173 | 54% helix, 12% strand | A0A0J9X267 |
| C | Hemagglutinin | protein | 325 | 10% helix, 38% strand | A0A0J9X268 |
| E | Hemagglutinin | protein | 325 | 9% helix, 40% strand | A0A0J9X268 |
| F | Hemagglutinin HA2 chain | protein | 172 | 57% helix, 12% strand | A0A0J9X267 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, E
- 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 | 886 | 0.85 | 0.87 | 107 | empty |
| 2 | 124 | 0.81 | 0.98 | 16 | empty |
| 3 | 148 | 0.79 | 0.96 | 22 | empty |
| 4 | 955 | 0.75 | 0.78 | 88 | empty |
| 5 | 263 | 0.73 | 0.87 | 33 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2742 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2725 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2709 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1368 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1303 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5T0D · Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2013) H6N1 influenza… · 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 A0A0J9X268
- Every structure of UniProt A0A0J9X267
- Elsewhere: RCSB PDB 5T0D · PDBe 5T0D · UniProt A0A0J9X268 · UniProt A0A0J9X267
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