MolNFT v2 · #24700 · protein
Structure of the hemagglutinin-neuraminidase from human parainfluenza virus type III: complex with NEU5AC2EN
1V3D · hemagglutinin-neuraminidase glycoprotein: “Structure of the hemagglutinin-neuraminidase from human parainfluenza virus type III: complex with NEU5AC2EN”. X-ray diffraction at 2.28, 4 ligands (NAG, DAN, CA), 11 pockets (best…
- PDB
- 1V3D
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.28
- Source
- Human parainfluenza virus 3
- Molecule
- hemagglutinin-neuraminidase glycoprotein
- EC
- 3.2.1.18
- Ligands
- NAG, DAN, CA, SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.28 · 1 distinct chain · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | hemagglutinin-neuraminidase glycoprotein (EC 3.2.1.18) | protein | 431 | 6% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.77 | 0.98 | 29 | empty |
| 2 | 422 | 0.75 | 0.85 | 66 | SO4 |
| 3 | 373 | 0.65 | 0.79 | 32 | DAN |
| 4 | 376 | 0.65 | 0.79 | 31 | SO4, DAN |
| 5 | 170 | 0.60 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1669 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1V3D · Structure of the hemagglutinin-neuraminidase from human parainfluenza virus type III… · 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
- Elsewhere: RCSB PDB 1V3D · PDBe 1V3D
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