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Parainfluenza virus 5 (SV5) hemagglutinin-neuraminidase (hn) with ligand dana (soaked with sialic acid, pH 8.0)
Analyse Parainfluenza virus 5 (SV5) hemagglutinin-neuraminidase (hn) with ligand dana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z50
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase
- EC
- 3.2.1.18
- UniProt
- P04850
- Ligands
- DAN, NAG, CA
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 448 | 8% helix, 46% strand | P04850 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.66 | 0.80 | 37 | DAN |
| 2 | 94 | 0.48 | 0.82 | 28 | empty |
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1Z50 · Parainfluenza Virus 5 (SV5) Hemagglutinin-Neuraminidase (HN) with ligand DANA (soaked… · 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 P04850
- Elsewhere: RCSB PDB 1Z50 · PDBe 1Z50 · UniProt P04850
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