Research workbench
Influenza hemagglutinin H1 mutant DH1 in complex with 6'SLN
Analyse Influenza hemagglutinin H1 mutant DH1 in complex with 6'SLN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VMC
- Type
- protein
- Length
- 1,454 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- Q9WFX3
- Ligands
- NAG, GAL, SIA, BMA
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 321 | 9% helix, 40% strand | Q9WFX3 |
| B, D | Hemagglutinin HA2 | protein | 164 | 54% helix, 16% strand | Q9WFX3 |
| F | Hemagglutinin HA2 | protein | 163 | 54% helix, 15% strand | Q9WFX3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C, E
- GAL · beta-D-galactopyranose · 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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.85 | 0.95 | 31 | empty |
| 2 | 1068 | 0.82 | 0.83 | 133 | empty |
| 3 | 145 | 0.80 | 0.96 | 27 | empty |
| 4 | 196 | 0.77 | 0.92 | 35 | empty |
| 5 | 914 | 0.74 | 0.78 | 94 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2864 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2828 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2824 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 1351 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1320 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5VMC · Influenza hemagglutinin H1 mutant DH1 in complex with 6'SLN · 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 Q9WFX3
- Elsewhere: RCSB PDB 5VMC · PDBe 5VMC · UniProt Q9WFX3
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