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Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 (PIV5) fusion protein
Analyse Structure of the cleavage-activated prefusion form of the parainfluenza virus 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GIP
- Type
- protein
- Length
- 1,368 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F2; Fusion glycoprotein F1
- UniProt
- P04849
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fusion glycoprotein F2 | protein | 81 | 40% helix, 32% strand | P04849 |
| D, E, F | Fusion glycoprotein F1 | protein | 375 | 34% helix, 29% strand | P04849 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, D, E, B, F, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.77 | 0.79 | 62 | empty |
| 2 | 1120 | 0.72 | 0.76 | 144 | empty |
| 3 | 820 | 0.71 | 0.76 | 92 | empty |
| 4 | 517 | 0.63 | 0.75 | 61 | empty |
| 5 | 309 | 0.53 | 0.74 | 47 | empty |
Interfaces
12 interfaces between chains.
- B–E · 4861 Ų buried · 81 hydrogen bonds · protein-protein
- A–D · 4690 Ų buried · 80 hydrogen bonds · protein-protein
- C–F · 4619 Ų buried · 67 hydrogen bonds · protein-protein
- D–F · 2424 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2378 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4GIP · Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 (PIV5)… · 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 P04849
- Elsewhere: RCSB PDB 4GIP · PDBe 4GIP · UniProt P04849
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