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Crystal structure of H10 hemagglutinin mutant (T193D-Q226L-G228S) from jiangxi-donghu (2013) H10N8 influenza virus in complex with 6'-slnln
Analyse Crystal structure of H10 hemagglutinin mutant (T193D-Q226L-G228S) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5THC
- Type
- protein
- Length
- 1,465 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- A0A0J9X252, A0A0J9X253
- Ligands
- NAG, SIA, GAL, BMA, MAN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 318 | 9% helix, 40% strand | A0A0J9X252 |
| B, D | Hemagglutinin HA2 chain | protein | 171 | 58% helix, 12% strand | A0A0J9X253 |
| F | Hemagglutinin HA2 chain | protein | 169 | 57% helix, 11% strand | A0A0J9X253 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, E, D
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains E, C
- GAL · beta-D-galactopyranose · sugar · chains E
- BMA · beta-D-mannopyranose · sugar
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.84 | 0.85 | 130 | empty |
| 2 | 365 | 0.84 | 0.93 | 38 | empty |
| 3 | 142 | 0.78 | 0.95 | 38 | empty |
| 4 | 175 | 0.77 | 0.93 | 32 | empty |
| 5 | 269 | 0.73 | 0.87 | 35 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3210 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3194 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 3175 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 1517 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1473 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5THC · Crystal structure of H10 hemagglutinin mutant (T193D-Q226L-G228S) from Jiangxi-Donghu… · 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 A0A0J9X252
- Every structure of UniProt A0A0J9X253
- Elsewhere: RCSB PDB 5THC · PDBe 5THC · UniProt A0A0J9X252 · UniProt A0A0J9X253
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