Research workbench
Crystal structure of H3 hemagglutinin with insertion of two amino acids in the 150-loop from the A/HONG KONG/1/1968 (H3N2) influenza virus
Analyse Crystal structure of H3 hemagglutinin with insertion of two amino acids in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5THF
- Type
- protein
- Length
- 1,488 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q91MA7
- Ligands
- NAG, BMA
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemagglutinin HA1 chain | protein | 319 | 10% helix, 41% strand | Q91MA7 |
| B | Hemagglutinin HA2 chain | protein | 172 | 54% helix, 13% strand | Q91MA7 |
| C | Hemagglutinin HA1 chain | protein | 318 | 10% helix, 41% strand | Q91MA7 |
| D | Hemagglutinin HA2 chain | protein | 184 | 51% helix, 14% strand | Q91MA7 |
| F | Hemagglutinin HA2 chain | protein | 176 | 50% helix, 15% strand | Q91MA7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, C, B, E, D, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.87 | 0.89 | 41 | empty |
| 2 | 250 | 0.84 | 0.95 | 30 | empty |
| 3 | 612 | 0.75 | 0.81 | 68 | empty |
| 4 | 834 | 0.74 | 0.79 | 83 | empty |
| 5 | 883 | 0.74 | 0.78 | 93 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2961 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2943 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2862 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 1592 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1580 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5THF · Crystal structure of H3 hemagglutinin with insertion of two amino acids in the 150-loop… · 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 Q91MA7
- Elsewhere: RCSB PDB 5THF · PDBe 5THF · UniProt Q91MA7
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