Research workbench
Structure of hemagglutinin with F95Y mutation of influenza virus B/LEE/40
Analyse Structure of hemagglutinin with F95Y mutation of influenza virus B/LEE/40 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NRL
- Type
- protein
- Length
- 1,531 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- P03460
- Ligands
- NAG, GAL, BGC, SIA, BMA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 341 | 8% helix, 36% strand | P03460 |
| B | Hemagglutinin HA2 chain | protein | 170 | 52% helix, 12% strand | P03460 |
| D, F | Hemagglutinin HA2 chain | protein | 169 | 51% helix, 13% strand | P03460 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 copies · chains A, B, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, C, E
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- BMA · beta-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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.89 | 0.91 | 166 | empty |
| 2 | 1020 | 0.88 | 0.89 | 91 | empty |
| 3 | 93 | 0.79 | 0.99 | 13 | empty |
| 4 | 98 | 0.63 | 0.89 | 31 | empty |
| 5 | 288 | 0.63 | 0.80 | 27 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2968 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2967 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2943 Ų buried · 51 hydrogen bonds · protein-protein
- B–F · 1540 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1498 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 4NRL · Structure of hemagglutinin with F95Y mutation of influenza virus B/Lee/40 · 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 P03460
- Elsewhere: RCSB PDB 4NRL · PDBe 4NRL · UniProt P03460
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