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The catalytic mechanism of human parainfluenza virus type 3 haemagglutinin-neuraminidase revealed
Analyse The catalytic mechanism of human parainfluenza virus type 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XJR
- Type
- protein
- Length
- 855 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase
- EC
- 3.2.1.18
- UniProt
- G8G134
- Ligands
- OEL, NAG, BMA, CA, SO4
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 429 | 6% helix, 47% strand | G8G134 |
| B | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 426 | 5% helix, 46% strand | G8G134 |
Ligands and binding sites
- OEL · (6R)-2,6-anhydro-3,4,5-trideoxy-6-[(2S)-2,3-dihydroxypropanoyl]-3-fluoro-5-[(2-methylpropanoyl)amino]-4-triaza-1,2-dien -2-ium-1-yl-L-gulonic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.66 | 0.80 | 32 | OEL |
| 2 | 338 | 0.64 | 0.80 | 32 | OEL |
| 3 | 152 | 0.59 | 0.83 | 25 | empty |
| 4 | 235 | 0.58 | 0.79 | 31 | empty |
| 5 | 164 | 0.57 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1805 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 4XJR · The catalytic mechanism of human parainfluenza virus type 3 haemagglutinin-neuraminidase… · 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 G8G134
- Elsewhere: RCSB PDB 4XJR · PDBe 4XJR · UniProt G8G134
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