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Crystal structure of mumps virus hemagglutinin-neuraminidase bound to the oligosaccharide portion of the GM2 ganglioside
Analyse Crystal structure of mumps virus hemagglutinin-neuraminidase bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JJM
- Type
- protein
- Length
- 904 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hn protein
- UniProt
- Q9WAF5
- Ligands
- NAG, BGC, GAL, SIA, SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hn protein | protein | 452 | 8% helix, 43% strand | Q9WAF5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.71 | 0.97 | 22 | empty |
| 2 | 372 | 0.66 | 0.80 | 44 | GAL, SIA, NAG |
| 3 | 331 | 0.63 | 0.79 | 40 | GAL, SIA, NAG |
| 4 | 144 | 0.52 | 0.80 | 30 | empty |
| 5 | 107 | 0.43 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1889 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6JJM · Crystal structure of Mumps virus hemagglutinin-neuraminidase bound to the oligosaccharide… · 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 Q9WAF5
- Elsewhere: RCSB PDB 6JJM · PDBe 6JJM · UniProt Q9WAF5
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