Research workbench
Crystal structure of hemagglutinin from an H7N9 influenza virus in complex with lsta
Analyse Crystal structure of hemagglutinin from an H7N9 influenza virus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N5K
- Type
- protein
- Length
- 974 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- R4NN21
- Ligands
- NAG, SIA, BMA, GAL
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin HA1 | protein | 318 | 8% helix, 39% strand | R4NN21 |
| B, D | Hemagglutinin HA2 | protein | 169 | 54% helix, 13% strand | R4NN21 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, D
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.63 | 0.82 | 25 | empty |
| 2 | 249 | 0.62 | 0.81 | 25 | empty |
| 3 | 104 | 0.48 | 0.80 | 25 | empty |
| 4 | 121 | 0.47 | 0.79 | 25 | empty |
| 5 | 85 | 0.43 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3180 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3131 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 218 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4N5K · Crystal structure of hemagglutinin from an H7N9 influenza virus in complex with LSTa · 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 R4NN21
- Elsewhere: RCSB PDB 4N5K · PDBe 4N5K · UniProt R4NN21
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