MolNFT v1 · #31882 · protein
Structure of the parainfluenza virus 5 F protein in its metastable, pre-fusion conformation
2B9B · Fusion glycoprotein F0: “Structure of the parainfluenza virus 5 F protein in its metastable, pre-fusion conformation”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.77). MolNFT v1 #31882 on GenesisL1: 3D…
- PDB
- 2B9B
- Type
- protein
- Length
- 1,441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0
- UniProt
- P04849
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion glycoprotein F0 | protein | 478 | 39% helix, 26% strand | P04849 |
| B | Fusion glycoprotein F0 | protein | 482 | 38% helix, 26% strand | P04849 |
| C | Fusion glycoprotein F0 | protein | 481 | 38% helix, 26% strand | P04849 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.77 | 0.79 | 60 | empty |
| 2 | 715 | 0.67 | 0.75 | 76 | empty |
| 3 | 582 | 0.63 | 0.75 | 57 | empty |
| 4 | 348 | 0.59 | 0.77 | 56 | empty |
| 5 | 319 | 0.54 | 0.75 | 50 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3094 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2916 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 2913 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 2B9B · Structure of the Parainfluenza Virus 5 F Protein in its Metastable, Pre-fusion… · 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 2B9B · PDBe 2B9B · UniProt P04849
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