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Crystal structure of a 2009 H1N1 influenza virus hemagglutinin with a stabilization mutation HA2 E47G
Analyse Crystal structure of a 2009 H1N1 influenza virus hemagglutinin with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M4Y
- Type
- protein
- Length
- 1,490 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 subunit; Hemagglutinin HA2 subunit
- UniProt
- C3W5S1
- Ligands
- NAG, BMA, MAN, FUL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 subunit | protein | 324 | 9% helix, 40% strand | C3W5S1 |
| C | Hemagglutinin HA1 subunit | protein | 323 | 9% helix, 41% strand | C3W5S1 |
| E | Hemagglutinin HA1 subunit | protein | 326 | 8% helix, 40% strand | C3W5S1 |
| B | Hemagglutinin HA2 subunit | protein | 175 | 56% helix, 14% strand | C3W5S1 |
| D, F | Hemagglutinin HA2 subunit | protein | 171 | 56% helix, 15% strand | C3W5S1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains C, E, A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUL · beta-L-fucopyranose · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.85 | 0.96 | 32 | empty |
| 2 | 919 | 0.84 | 0.86 | 142 | empty |
| 3 | 180 | 0.75 | 0.91 | 34 | empty |
| 4 | 987 | 0.74 | 0.77 | 108 | empty |
| 5 | 271 | 0.74 | 0.87 | 44 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2839 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2819 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2786 Ų buried · 42 hydrogen bonds · protein-protein
- B–F · 1363 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1311 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4M4Y · Crystal structure of a 2009 H1N1 influenza virus hemagglutinin with a stabilization… · 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 C3W5S1
- Elsewhere: RCSB PDB 4M4Y · PDBe 4M4Y · UniProt C3W5S1
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