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Structure of the parainfluenza virus 5 (PIV5) hemagglutinin- neuraminidase (hn) ectodomain
Analyse Structure of the parainfluenza virus 5 (PIV5) hemagglutinin- neuraminidase (hn)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JF7
- Type
- protein
- Length
- 1,987 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase
- EC
- 3.2.1.18
- UniProt
- P04850
- Ligands
- NAG, MAN, CA, SO4
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 492 | 13% helix, 42% strand | P04850 |
| A | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 501 | 13% helix, 41% strand | P04850 |
| B | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 501 | 16% helix, 41% strand | P04850 |
| C | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 493 | 15% helix, 42% strand | P04850 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains D, A, B, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 4 copies · chains D, A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.82 | 0.90 | 57 | empty |
| 2 | 98 | 0.77 | 0.98 | 21 | empty |
| 3 | 62 | 0.74 | 0.99 | 21 | empty |
| 4 | 64 | 0.74 | 0.99 | 23 | empty |
| 5 | 62 | 0.70 | 0.96 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3257 Ų buried · 40 hydrogen bonds · protein-protein
- D–C · 3222 Ų buried · 33 hydrogen bonds · protein-protein
- D–A · 1555 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 754 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4JF7 · Structure of the parainfluenza virus 5 (PIV5) hemagglutinin-neuraminidase (HN) ectodomain · the same entry in another collection · chain D against D, 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 4JF7 · PDBe 4JF7 · UniProt P04850
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