MolNFT v1 · #134842 · protein
Crystal structure of H10 hemagglutinin mutant (K158AA-Q226L-G228S) from jiangxi-donghu (2013) H10N8 influenza virus
5TH0 · Hemagglutinin HA1 chain: “Crystal structure of H10 hemagglutinin mutant (K158AA-Q226L-G228S) from jiangxi-donghu (2013) H10N8 influenza…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5TH0
- Type
- protein
- Length
- 1,464 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, BMA, MAN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemagglutinin HA1 chain | protein | 318 | 9% helix, 42% strand | A0A0J9X252 |
| B | Hemagglutinin HA2 chain | protein | 171 | 58% helix, 13% strand | A0A0J9X253 |
| C | Hemagglutinin HA1 chain | protein | 319 | 9% helix, 40% strand | A0A0J9X252 |
| D | Hemagglutinin HA2 chain | protein | 168 | 59% helix, 13% strand | A0A0J9X253 |
| F | Hemagglutinin HA2 chain | protein | 170 | 56% helix, 14% strand | A0A0J9X253 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, E, B, D
- 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.85 | 0.96 | 27 | empty |
| 2 | 420 | 0.85 | 0.93 | 42 | empty |
| 3 | 1128 | 0.76 | 0.78 | 121 | empty |
| 4 | 89 | 0.74 | 0.96 | 20 | empty |
| 5 | 191 | 0.73 | 0.90 | 29 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3216 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 3165 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3131 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1523 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1489 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5TH0 · Crystal structure of H10 hemagglutinin mutant (K158aA-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 5TH0 · PDBe 5TH0 · UniProt A0A0J9X252 · UniProt A0A0J9X253
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