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Crystal structure of influenza B virus hemagglutinin in complex with lsta receptor analog
Analyse Crystal structure of influenza B virus hemagglutinin in complex with lsta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RFT
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Influenza B hemagglutinin (ha)
- UniProt
- Q84097
- Ligands
- NAG, GAL, BGC, NDG, SIA
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Influenza B hemagglutinin (ha) | protein | 342 | 8% helix, 31% strand | Q84097 |
| B | Influenza B hemagglutinin (ha) | protein | 169 | 48% helix, 10% strand | Q84097 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.59 | 0.86 | 28 | empty |
| 2 | 118 | 0.44 | 0.77 | 23 | empty |
| 3 | 97 | 0.40 | 0.77 | 16 | empty |
| 4 | 55 | 0.38 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3054 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 2RFT · Crystal structure of influenza B virus hemagglutinin in complex with LSTa receptor analog · 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 Q84097
- Elsewhere: RCSB PDB 2RFT · PDBe 2RFT · UniProt Q84097
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