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Crystal structure of mumps virus hemagglutinin-neuraminidase bound to 3-sialyllactose
Analyse Crystal structure of mumps virus hemagglutinin-neuraminidase bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B2D
- Type
- protein
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hn protein
- EC
- 3.2.1.18
- UniProt
- Q9WAF5
- Ligands
- NAG, GLC, GAL, SIA, SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hn protein (EC 3.2.1.18) | protein | 450 | 7% helix, 42% strand | Q9WAF5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- GLC · alpha-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 · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.70 | 0.98 | 20 | empty |
| 2 | 363 | 0.63 | 0.78 | 39 | GAL, SIA |
| 3 | 362 | 0.63 | 0.78 | 35 | GLC, GAL, SIA |
| 4 | 140 | 0.52 | 0.80 | 26 | empty |
| 5 | 111 | 0.51 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1828 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5B2D · Crystal structure of Mumps virus hemagglutinin-neuraminidase bound to 3-sialyllactose · 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 5B2D · PDBe 5B2D · UniProt Q9WAF5
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